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"	4901
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4691
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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: 1.14.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.14.0.tar.gz

StartedAt: 2025-11-01 16:01:14 -0400 (Sat, 01 Nov 2025)

EndedAt: 2025-11-01 16:02:07 -0400 (Sat, 01 Nov 2025)

EllapsedTime: 53.5 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 [2025-11-01 16:01:58.910][biodb::testContext]
biodb.INFO [2025-11-01 16:01:58.913][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:01:58.914][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2025-11-01 16:01:58.915][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:01:58.916][biodb::testContext]
biodb.INFO [2025-11-01 16:01:58.921][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:01:58.923][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-11-01 16:01:58.930][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:01:58.931][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-01 16:01:58.932][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-01 16:01:58.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:58.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:58.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:58.935][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-01 16:01:58.951][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-01 16:01:58.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:58.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:58.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:58.964][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-01 16:01:58.965][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-01 16:01:58.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:58.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:58.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:58.968][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-01 16:01:58.969][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-01 16:01:58.970][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-01 16:01:58.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:58.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:58.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:58.973][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-01 16:01:58.974][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-01 16:01:58.975][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-01 16:01:58.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:58.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:58.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:58.978][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-01 16:01:58.979][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-01 16:01:58.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:58.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:58.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:58.982][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-01 16:01:58.983][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-01 16:01:58.984][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-01 16:01:58.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:58.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:58.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:58.987][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-01 16:01:58.988][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-01 16:01:58.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:58.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:58.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:58.991][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-01 16:01:58.992][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-01 16:01:58.993][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-01 16:01:58.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:58.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:58.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:58.996][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:01:58.997][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-01 16:01:58.998][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-01 16:01:58.999][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-01 16:01:59.000][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-01 16:01:59.001][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-01 16:01:59.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.005][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-01 16:01:59.006][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-01 16:01:59.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.009][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-01 16:01:59.010][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-01 16:01:59.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.013][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-01 16:01:59.014][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-01 16:01:59.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.017][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-01 16:01:59.018][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-01 16:01:59.019][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-01 16:01:59.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.021][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[2025-11-01 16:01:59.022][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:01:59.023][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-01 16:01:59.044][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-01 16:01:59.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.047][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-01 16:01:59.048][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-01 16:01:59.049][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-01 16:01:59.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.054][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-01 16:01:59.082][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.095][self$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[2025-11-01 16:01:59.096][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.097][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:01:59.098][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.099][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.100][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.101][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.102][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:01:59.102][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:01:59.103][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.104][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-01 16:01:59.105][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:01:59.106][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.107][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.108][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:01:59.108][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:01:59.108][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:01:59.108][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:01:59.108][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:01:59.109][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:01:59.109][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.110][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.111][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:01:59.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.114][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.114][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.115][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:01:59.116][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:01:59.117][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.118][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.119][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-01 16:01:59.125][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.126][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:01:59.127][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.127][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:01:59.128][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.129][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.130][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.131][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.132][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:01:59.133][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:01:59.133][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.134][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-01 16:01:59.135][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:01:59.136][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.137][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.138][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:01:59.138][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:01:59.138][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:01:59.138][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:01:59.138][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:01:59.139][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:01:59.140][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.140][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.141][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:01:59.142][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.143][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.144][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.145][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.145][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:01:59.146][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:01:59.147][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.148][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.149][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-01 16:01:59.151][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.151][self$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[2025-11-01 16:01:59.152][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.153][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:01:59.154][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.155][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.156][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.157][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.157][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:01:59.158][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:01:59.159][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.160][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-01 16:01:59.161][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:01:59.162][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.163][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.164][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.165][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:01:59.165][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.166][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.167][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:01:59.168][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.169][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.169][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.170][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.171][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:01:59.172][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:01:59.173][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.174][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.175][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-01 16:01:59.176][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.177][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:01:59.178][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.179][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:01:59.180][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.181][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.182][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.183][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.183][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:01:59.184][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:01:59.185][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.186][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-01 16:01:59.187][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:01:59.188][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.189][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.190][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.191][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:01:59.191][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.192][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.193][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:01:59.194][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.195][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.196][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.196][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.197][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:01:59.198][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:01:59.199][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.200][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.203][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:01:59.204][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.256][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[2025-11-01 16:01:59.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.272][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-01 16:01:59.276][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-01 16:01:59.277][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-01 16:01:59.278][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-01 16:01:59.280][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-01 16:01:59.281][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-01 16:01:59.282][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-01 16:01:59.283][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-01 16:01:59.285][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-01 16:01:59.286][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-01 16:01:59.287][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-01 16:01:59.288][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-01 16:01:59.289][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-01 16:01:59.291][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-01 16:01:59.292][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-01 16:01:59.293][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:01:59.294][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-01 16:01:59.296][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-01 16:01:59.297][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-01 16:01:59.298][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-01 16:01:59.299][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-01 16:01:59.300][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-01 16:01:59.302][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-01 16:01:59.303][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-01 16:01:59.304][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-01 16:01:59.305][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-01 16:01:59.306][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-01 16:01:59.308][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-01 16:01:59.309][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-01 16:01:59.310][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-01 16:01:59.311][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-01 16:01:59.313][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-01 16:01:59.314][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-01 16:01:59.315][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-01 16:01:59.316][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-01 16:01:59.317][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-01 16:01:59.318][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-01 16:01:59.320][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-01 16:01:59.321][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-01 16:01:59.322][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-01 16:01:59.323][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-01 16:01:59.325][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-01 16:01:59.326][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-01 16:01:59.327][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-01 16:01:59.328][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-01 16:01:59.329][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-01 16:01:59.331][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-01 16:01:59.332][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-01 16:01:59.333][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-01 16:01:59.334][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-01 16:01:59.335][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-01 16:01:59.337][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-01 16:01:59.338][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-01 16:01:59.339][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-01 16:01:59.340][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-01 16:01:59.341][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-01 16:01:59.343][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-01 16:01:59.344][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-01 16:01:59.345][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-01 16:01:59.346][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-01 16:01:59.348][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-01 16:01:59.349][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-01 16:01:59.350][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-01 16:01:59.351][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-01 16:01:59.352][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-01 16:01:59.354][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-01 16:01:59.355][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-01 16:01:59.356][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-01 16:01:59.357][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-01 16:01:59.358][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-01 16:01:59.359][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-01 16:01:59.361][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-01 16:01:59.362][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-01 16:01:59.363][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-01 16:01:59.364][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-01 16:01:59.366][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-01 16:01:59.367][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-01 16:01:59.368][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-01 16:01:59.369][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-01 16:01:59.370][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-01 16:01:59.372][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-01 16:01:59.373][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-01 16:01:59.374][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-01 16:01:59.379][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-01 16:01:59.381][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:01:59.383][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:01:59.384][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.386][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.406][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[2025-11-01 16:01:59.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.422][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[2025-11-01 16:01:59.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.473][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[2025-11-01 16:01:59.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.478][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[2025-11-01 16:01:59.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:01:59.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:01:59.486][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-11-01 16:01:59.495][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-11-01 16:01:59.497][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.498][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-11-01 16:01:59.499][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.499][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:01:59.500][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.501][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.502][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.503][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.504][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-11-01 16:01:59.505][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:01:59.506][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.507][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-11-01 16:01:59.507][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:01:59.508][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-11-01 16:01:59.508][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-11-01 16:01:59.509][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.510][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.511][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-01 16:01:59.512][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.513][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.514][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:01:59.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.516][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.517][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-11-01 16:01:59.517][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-11-01 16:01:59.518][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:01:59.519][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:01:59.520][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.520][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.522][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-11-01 16:01:59.523][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.524][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-11-01 16:01:59.525][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.526][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:01:59.527][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.528][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.529][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.529][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.530][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-01 16:01:59.531][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:01:59.532][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.533][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-11-01 16:01:59.534][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:01:59.535][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-11-01 16:01:59.535][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-11-01 16:01:59.535][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-11-01 16:01:59.535][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-11-01 16:01:59.535][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-11-01 16:01:59.535][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-11-01 16:01:59.536][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.537][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:01:59.537][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-01 16:01:59.538][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.539][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.540][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:01:59.541][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.542][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.542][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.543][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:01:59.543][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-01 16:01:59.544][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:01:59.545][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:01:59.546][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.547][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.548][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-11-01 16:01:59.549][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.550][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-11-01 16:01:59.555][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.556][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:01:59.557][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.558][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.559][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.560][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.560][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-01 16:01:59.561][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:01:59.562][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.563][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-11-01 16:01:59.564][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:01:59.565][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-01 16:01:59.565][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:01:59.565][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:01:59.565][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:01:59.565][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:01:59.565][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:01:59.565][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:01:59.565][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:01:59.565][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:01:59.565][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:01:59.565][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-11-01 16:01:59.565][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:01:59.565][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:01:59.565][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:01:59.566][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.567][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:01:59.567][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:01:59.567][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:01:59.568][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-01 16:01:59.569][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.569][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.570][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:01:59.571][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.572][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.573][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.574][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:01:59.574][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-01 16:01:59.574][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-01 16:01:59.574][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:01:59.575][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:01:59.576][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.577][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-01 16:01:59.578][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-11-01 16:01:59.580][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.581][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-11-01 16:01:59.581][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.582][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:01:59.583][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.584][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.585][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.586][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.587][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-01 16:01:59.588][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:01:59.589][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.589][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-11-01 16:01:59.590][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:01:59.591][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-11-01 16:01:59.591][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-01 16:01:59.592][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:01:59.593][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:01:59.594][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-01 16:01:59.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.597][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:01:59.597][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:01:59.598][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:01:59.599][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:01:59.600][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:01:59.600][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-01 16:01:59.600][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-01 16:01:59.601][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:01:59.602][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:01:59.603][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:01:59.603][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-01 16:01:59.609][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-11-01 16:01:59.610][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-01 16:01:59.611][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:01:59.613][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-11-01 16:01:59.614][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-01 16:01:59.616][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-11-01 16:01:59.634][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-11-01 16:01:59.648][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2025-11-01 16:01:59.656][biodb::testThat]
biodb.INFO [2025-11-01 16:01:59.657][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-01 16:01:59.658][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:01:59.659][biodb::testThat]
biodb.TRACE[2025-11-01 16:01:59.663][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2025-11-01 16:01:59.664][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-11-01 16:01:59.667][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-11-01 16:01:59.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-01 16:01:59.674][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:01:59.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:01:59.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:01:59.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:01:59.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:01:59.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-01 16:01:59.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.721][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-11-01 16:01:59.741][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:01:59.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.742][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.765][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-11-01 16:01:59.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:01:59.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.769][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:01:59.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:01:59.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.773][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:01:59.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:01:59.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.780][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:01:59.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:01:59.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:01:59.872][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2025-11-01 16:01:59.874][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:01:59.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:01:59.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.878][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:01:59.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:01:59.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.900][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:01:59.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:01:59.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.904][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:01:59.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:01:59.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.908][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-01 16:01:59.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-01 16:01:59.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.911][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-01 16:01:59.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-01 16:01:59.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.931][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:01:59.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:01:59.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.962][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:01:59.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:01:59.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.966][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:01:59.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:01:59.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.974][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:01:59.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:01:59.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.996][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:01:59.996][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:01:59.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:01:59.998][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:01:59.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.011][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-11-01 16:02:00.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.015][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.018][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.022][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-11-01 16:02:00.023][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.025][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.026][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-11-01 16:02:00.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.037][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.038][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.040][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.045][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.046][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.047][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.063][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2025-11-01 16:02:00.098][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-11-01 16:02:00.099][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-11-01 16:02:00.101][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-01 16:02:00.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:00.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:00.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.109][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-01 16:02:00.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.138][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-11-01 16:02:00.139][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.141][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.142][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-11-01 16:02:00.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.146][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:00.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:00.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.149][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:00.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:00.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.156][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:00.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:00.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:02:00.181][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2025-11-01 16:02:00.204][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.208][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.211][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:00.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:00.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.215][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:00.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:00.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.218][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:00.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:00.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.222][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:00.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:00.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.234][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:00.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:00.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.265][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:00.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:00.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.268][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:00.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:00.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.272][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:00.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:00.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.305][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.306][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.308][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.322][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-11-01 16:02:00.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.327][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.330][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.334][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-11-01 16:02:00.335][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.337][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.337][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-11-01 16:02:00.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.349][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.350][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:00.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.352][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:00.357][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:00.358][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:00.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:00.360][ef$get] fields variable is a list.
biodb.INFO [2025-11-01 16:02:00.368][biodb::testThat]
biodb.INFO [2025-11-01 16:02:00.369][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-01 16:02:00.370][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:00.371][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:00.373][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2025-11-01 16:02:00.378][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2025-11-01 16:02:00.381][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-11-01 16:02:00.382][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:00.383][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-11-01 16:02:00.384][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:00.385][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:00.423][biodb::testThat]
biodb.INFO [2025-11-01 16:02:00.424][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-01 16:02:00.425][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:00.425][biodb::testThat]
biodb.INFO [2025-11-01 16:02:00.432][biodb::testThat]
biodb.INFO [2025-11-01 16:02:00.432][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-01 16:02:00.439][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:00.440][biodb::testThat]
biodb.WARN [2025-11-01 16:02:00.456][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-11-01 16:02:00.476][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-11-01 16:02:00.485][biodb::testThat]
biodb.INFO [2025-11-01 16:02:00.486][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-01 16:02:00.487][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:00.488][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:00.503][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2025-11-01 16:02:00.547][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-11-01 16:02:00.572][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-11-01 16:02:00.574][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:00.575][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-11-01 16:02:00.576][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:00.576][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:00.608][biodb::testThat]
biodb.INFO [2025-11-01 16:02:00.609][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-01 16:02:00.610][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:00.611][biodb::testThat]
biodb.INFO [2025-11-01 16:02:00.629][biodb::testThat]
biodb.INFO [2025-11-01 16:02:00.630][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-01 16:02:00.631][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:00.631][biodb::testThat]
biodb.INFO [2025-11-01 16:02:00.639][biodb::testThat]
biodb.INFO [2025-11-01 16:02:00.640][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-01 16:02:00.641][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:00.642][biodb::testThat]
biodb.INFO [2025-11-01 16:02:00.656][biodb::testThat]
biodb.INFO [2025-11-01 16:02:00.657][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-01 16:02:00.658][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:00.658][biodb::testThat]
biodb.INFO [2025-11-01 16:02:00.665][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-01 16:02:00.666][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-11-01 16:02:00.667][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-01 16:02:00.668][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:00.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:00.670][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.671][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-11-01 16:02:00.683][biodb::testContext]
biodb.INFO [2025-11-01 16:02:00.684][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:02:00.685][biodb::testContext] Test context - Gene long tests
biodb.INFO [2025-11-01 16:02:00.686][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:02:00.687][biodb::testContext]
biodb.INFO [2025-11-01 16:02:00.689][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:02:00.690][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-11-01 16:02:00.694][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:00.695][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-01 16:02:00.696][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-01 16:02:00.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.699][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-01 16:02:00.700][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-01 16:02:00.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.703][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-01 16:02:00.704][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-01 16:02:00.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.708][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-01 16:02:00.709][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-01 16:02:00.709][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-01 16:02:00.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.713][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-01 16:02:00.714][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-01 16:02:00.715][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-01 16:02:00.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.718][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-01 16:02:00.719][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-01 16:02:00.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.723][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-01 16:02:00.723][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-01 16:02:00.724][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-01 16:02:00.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.728][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-01 16:02:00.729][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-01 16:02:00.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.732][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-01 16:02:00.733][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-01 16:02:00.739][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-01 16:02:00.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.742][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:02:00.743][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-01 16:02:00.744][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-01 16:02:00.745][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-01 16:02:00.746][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-01 16:02:00.746][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-01 16:02:00.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.750][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-01 16:02:00.751][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-01 16:02:00.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.754][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-01 16:02:00.755][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-01 16:02:00.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.758][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-01 16:02:00.759][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-01 16:02:00.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.762][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[2025-11-01 16:02:00.762][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-01 16:02:00.763][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-01 16:02:00.764][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-01 16:02:00.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.767][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:02:00.768][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-01 16:02:00.788][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-01 16:02:00.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.791][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-01 16:02:00.792][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-01 16:02:00.793][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-01 16:02:00.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.797][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-01 16:02:00.798][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:00.799][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-01 16:02:00.800][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.801][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:00.802][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.803][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:00.804][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:00.805][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:00.806][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:02:00.806][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:00.807][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.808][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-01 16:02:00.809][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:00.810][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:00.811][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.812][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:00.812][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:00.812][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:00.812][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:02:00.812][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:02:00.813][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:00.814][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:00.815][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:00.815][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:00.816][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:00.817][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:00.818][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:00.819][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:00.820][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:00.821][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:00.821][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:00.822][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:00.823][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-01 16:02:00.825][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:00.826][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:02:00.827][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.828][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:00.829][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.830][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:00.830][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:00.831][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:00.832][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:02:00.833][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:00.834][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.835][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-01 16:02:00.836][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:00.837][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:00.838][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.839][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:00.839][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:00.839][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:00.839][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:02:00.839][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:02:00.840][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:00.840][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:00.841][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:00.842][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:00.843][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:00.844][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:00.845][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:00.846][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:00.846][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:00.847][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:00.848][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:00.849][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:00.850][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-01 16:02:00.852][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.853][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-01 16:02:00.854][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.854][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:00.855][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.856][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:00.857][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:00.858][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:00.863][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:02:00.864][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:00.865][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:00.866][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-01 16:02:00.867][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:00.868][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:00.869][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.870][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:00.871][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:00.872][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:00.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:00.873][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:00.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:00.875][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:00.876][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:00.877][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:00.878][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:00.878][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:00.879][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:00.880][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:00.881][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-01 16:02:00.883][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.884][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:02:00.885][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.885][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:00.886][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.887][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:00.888][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:00.889][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:00.890][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:02:00.891][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:00.892][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:00.893][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-01 16:02:00.894][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:00.895][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:00.895][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:00.896][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:00.897][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:00.898][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:00.899][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:00.900][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:00.901][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:00.902][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:00.902][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:00.903][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:00.904][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:00.905][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:00.906][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:00.907][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:00.908][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:00.909][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.938][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.DEBUG[2025-11-01 16:02:00.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.947][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[2025-11-01 16:02:00.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.976][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[2025-11-01 16:02:00.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:00.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:00.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:00.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:00.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:00.981][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-01 16:02:00.982][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-01 16:02:00.983][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-01 16:02:00.984][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-01 16:02:00.986][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-01 16:02:00.987][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-01 16:02:00.988][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-01 16:02:00.989][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-01 16:02:00.991][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-01 16:02:00.992][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-01 16:02:00.993][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-01 16:02:00.994][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-01 16:02:00.996][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-01 16:02:00.997][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-01 16:02:00.998][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-01 16:02:00.999][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:02:01.001][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-01 16:02:01.002][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-01 16:02:01.003][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-01 16:02:01.004][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-01 16:02:01.006][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-01 16:02:01.007][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-01 16:02:01.008][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-01 16:02:01.009][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-01 16:02:01.010][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-01 16:02:01.012][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-01 16:02:01.013][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-01 16:02:01.014][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-01 16:02:01.015][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-01 16:02:01.017][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-01 16:02:01.018][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-01 16:02:01.019][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-01 16:02:01.020][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-01 16:02:01.022][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-01 16:02:01.023][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-01 16:02:01.024][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-01 16:02:01.025][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-01 16:02:01.027][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-01 16:02:01.028][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-01 16:02:01.029][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-01 16:02:01.030][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-01 16:02:01.032][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-01 16:02:01.033][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-01 16:02:01.034][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-01 16:02:01.036][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-01 16:02:01.037][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-01 16:02:01.038][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-01 16:02:01.039][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-01 16:02:01.041][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-01 16:02:01.042][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-01 16:02:01.043][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-01 16:02:01.044][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-01 16:02:01.046][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-01 16:02:01.047][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-01 16:02:01.048][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-01 16:02:01.049][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-01 16:02:01.051][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-01 16:02:01.052][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-01 16:02:01.053][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-01 16:02:01.054][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-01 16:02:01.056][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-01 16:02:01.057][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-01 16:02:01.058][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-01 16:02:01.059][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-01 16:02:01.061][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-01 16:02:01.062][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-01 16:02:01.063][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-01 16:02:01.064][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-01 16:02:01.065][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-01 16:02:01.067][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-01 16:02:01.073][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-01 16:02:01.074][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-01 16:02:01.075][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-01 16:02:01.076][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-01 16:02:01.078][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-01 16:02:01.079][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-01 16:02:01.080][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-01 16:02:01.081][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-01 16:02:01.083][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-01 16:02:01.084][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-01 16:02:01.085][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-01 16:02:01.086][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-01 16:02:01.088][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-01 16:02:01.089][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-01 16:02:01.090][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:02:01.091][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:01.092][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.094][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.185][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[2025-11-01 16:02:01.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.192][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-11-01 16:02:01.194][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-11-01 16:02:01.196][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.197][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-11-01 16:02:01.197][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.198][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:01.199][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.200][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:01.201][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.202][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:01.203][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-11-01 16:02:01.204][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:01.205][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.206][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-11-01 16:02:01.207][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:01.207][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-11-01 16:02:01.207][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-11-01 16:02:01.208][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:01.209][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:01.210][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-01 16:02:01.211][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:01.212][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:01.213][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:01.214][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:01.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:01.215][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:01.216][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-11-01 16:02:01.216][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-11-01 16:02:01.217][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:01.218][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:01.219][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.220][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:01.221][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-11-01 16:02:01.222][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.223][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-11-01 16:02:01.224][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.225][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:01.226][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.227][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:01.228][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.229][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:01.230][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-01 16:02:01.230][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:01.231][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.232][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-11-01 16:02:01.233][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:01.234][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-11-01 16:02:01.234][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-11-01 16:02:01.234][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-11-01 16:02:01.234][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-11-01 16:02:01.234][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-11-01 16:02:01.234][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-11-01 16:02:01.235][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:01.236][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:01.237][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-01 16:02:01.238][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:01.239][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:01.240][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:01.241][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:01.241][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:01.242][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:01.243][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:01.243][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-01 16:02:01.244][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:01.245][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:01.246][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.247][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:01.248][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-11-01 16:02:01.249][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:01.250][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-11-01 16:02:01.251][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.252][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:01.253][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.254][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:01.255][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.256][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:01.257][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-01 16:02:01.258][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:01.258][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.259][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-11-01 16:02:01.260][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:01.261][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-01 16:02:01.261][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:01.261][self$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[2025-11-01 16:02:01.261][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:01.261][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:01.261][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:01.261][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:01.261][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:01.261][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:01.261][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:01.261][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-11-01 16:02:01.261][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:01.261][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:01.261][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:01.262][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:01.263][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:01.263][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:01.263][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:01.264][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-01 16:02:01.265][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:01.266][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:01.267][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:01.268][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:01.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:01.269][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:01.270][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:01.270][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-01 16:02:01.270][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-01 16:02:01.271][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:01.272][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:01.273][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.274][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-01 16:02:01.275][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-11-01 16:02:01.277][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.277][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-11-01 16:02:01.283][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.284][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:01.285][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.285][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:01.286][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.287][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:01.288][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-01 16:02:01.289][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:01.290][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.291][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-11-01 16:02:01.292][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:01.293][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-11-01 16:02:01.293][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-01 16:02:01.294][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:01.295][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:01.296][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-01 16:02:01.296][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:01.298][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:01.299][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:01.300][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:01.300][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:01.301][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:01.302][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:01.302][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-01 16:02:01.302][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-01 16:02:01.303][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:01.304][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:01.305][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.306][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-01 16:02:01.307][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-11-01 16:02:01.309][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-01 16:02:01.311][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:02:01.313][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-11-01 16:02:01.314][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-01 16:02:01.316][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-11-01 16:02:01.324][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2025-11-01 16:02:01.401][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2025-11-01 16:02:01.405][biodb::testThat]
biodb.INFO [2025-11-01 16:02:01.406][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-01 16:02:01.407][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:01.408][biodb::testThat]
biodb.TRACE[2025-11-01 16:02:01.413][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2025-11-01 16:02:01.414][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-11-01 16:02:01.417][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-11-01 16:02:01.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-01 16:02:01.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.427][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-01 16:02:01.439][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:01.440][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:01.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.442][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:01.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:01.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.447][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:01.448][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:01.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.450][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.452][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:01.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:01.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.455][ef$get] Asked field names are: location.
biodb.TRACE[2025-11-01 16:02:01.456][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-11-01 16:02:01.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.458][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.459][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-11-01 16:02:01.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-11-01 16:02:01.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.463][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-11-01 16:02:01.464][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-11-01 16:02:01.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.466][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.467][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-11-01 16:02:01.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-11-01 16:02:01.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.471][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-11-01 16:02:01.472][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:01.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.474][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.475][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-11-01 16:02:01.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:01.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.479][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-11-01 16:02:01.480][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-11-01 16:02:01.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.481][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.484][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-11-01 16:02:01.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-11-01 16:02:01.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.496][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:01.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:01.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.499][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-11-01 16:02:01.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-11-01 16:02:01.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.503][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-11-01 16:02:01.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-11-01 16:02:01.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:01.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:01.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.510][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-11-01 16:02:01.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-11-01 16:02:01.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:01.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:01.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:01.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:01.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:01.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:01.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:01.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:01.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:01.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:01.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:01.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:01.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:02:01.534][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2025-11-01 16:02:01.536][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:01.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:01.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.540][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:01.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:01.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.543][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:01.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:01.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.547][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:01.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:01.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:01.550][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:01.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:01.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:02:01.554][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-11-01 16:02:01.583][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-11-01 16:02:01.596][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2025-11-01 16:02:01.597][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2025-11-01 16:02:01.601][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-11-01 16:02:01.602][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-11-01 16:02:01.603][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:01.604][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-11-01 16:02:01.605][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:01.606][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:01.619][biodb::testThat]
biodb.INFO [2025-11-01 16:02:01.620][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-01 16:02:01.621][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:01.622][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:01.624][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2025-11-01 16:02:01.625][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2025-11-01 16:02:01.626][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-11-01 16:02:01.627][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:01.628][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:01.629][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:01.630][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:01.631][private$retrieveContents] Get entry content(s) for 8 id(s)...
biodb.INFO [2025-11-01 16:02:01.647][biodb::testThat]
biodb.INFO [2025-11-01 16:02:01.648][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-01 16:02:01.649][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:01.649][biodb::testThat]
biodb.TRACE[2025-11-01 16:02:01.652][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:01.653][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:01.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:01.655][ef$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:02:01.656][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2025-11-01 16:02:01.665][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-11-01 16:02:01.665][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-11-01 16:02:01.667][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-11-01 16:02:01.668][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:01.669][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:01.670][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:01.675][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:01.690][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-11-01 16:02:01.718][biodb::testThat]
biodb.INFO [2025-11-01 16:02:01.719][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-01 16:02:01.720][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:01.721][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:01.728][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-11-01 16:02:01.729][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-11-01 16:02:01.730][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-11-01 16:02:01.731][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:01.732][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:01.733][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:01.734][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:01.735][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-11-01 16:02:01.749][biodb::testThat]
biodb.INFO [2025-11-01 16:02:01.750][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-01 16:02:01.751][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:01.752][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:01.755][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-11-01 16:02:01.761][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-11-01 16:02:01.762][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-11-01 16:02:01.763][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:01.764][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:01.765][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:01.766][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:01.767][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-11-01 16:02:01.783][biodb::testThat]
biodb.INFO [2025-11-01 16:02:01.784][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-01 16:02:01.785][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:01.785][biodb::testThat]
biodb.INFO [2025-11-01 16:02:01.798][biodb::testThat]
biodb.INFO [2025-11-01 16:02:01.799][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-01 16:02:01.800][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:01.801][biodb::testThat]
biodb.INFO [2025-11-01 16:02:01.808][biodb::testThat]
biodb.INFO [2025-11-01 16:02:01.809][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-01 16:02:01.810][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:01.811][biodb::testThat]
biodb.INFO [2025-11-01 16:02:01.824][biodb::testThat]
biodb.INFO [2025-11-01 16:02:01.825][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-01 16:02:01.826][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:01.827][biodb::testThat]
biodb.INFO [2025-11-01 16:02:01.833][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-01 16:02:01.834][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2025-11-01 16:02:01.835][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-11-01 16:02:01.836][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-01 16:02:01.837][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:01.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:01.838][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:01.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:01.840][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-11-01 16:02:01.844][biodb::testContext]
biodb.INFO [2025-11-01 16:02:01.845][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:02:01.846][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2025-11-01 16:02:01.847][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:02:01.848][biodb::testContext]
biodb.INFO [2025-11-01 16:02:01.850][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:02:01.851][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-11-01 16:02:01.859][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:01.860][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-01 16:02:01.861][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-01 16:02:01.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.865][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-01 16:02:01.866][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-01 16:02:01.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.869][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-01 16:02:01.870][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-01 16:02:01.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.873][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-01 16:02:01.874][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-01 16:02:01.875][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-01 16:02:01.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.878][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-01 16:02:01.879][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-01 16:02:01.880][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-01 16:02:01.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.883][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[2025-11-01 16:02:01.883][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-01 16:02:01.884][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-01 16:02:01.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.888][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-01 16:02:01.889][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-01 16:02:01.890][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-01 16:02:01.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.893][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-01 16:02:01.894][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-01 16:02:01.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.898][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-01 16:02:01.899][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-01 16:02:01.900][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-01 16:02:01.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.903][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:02:01.904][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-01 16:02:01.905][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-01 16:02:01.906][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-01 16:02:01.907][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-01 16:02:01.908][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-01 16:02:01.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.913][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-01 16:02:01.914][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-01 16:02:01.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.918][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-01 16:02:01.920][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-01 16:02:01.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.925][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-01 16:02:01.927][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-01 16:02:01.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.931][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-01 16:02:01.933][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-01 16:02:01.935][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-01 16:02:01.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.940][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:02:01.942][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-01 16:02:01.972][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-01 16:02:01.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.976][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-01 16:02:01.977][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-01 16:02:01.978][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-01 16:02:01.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:01.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:01.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:01.981][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-01 16:02:01.983][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:01.984][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-01 16:02:01.985][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.986][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:01.987][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:01.988][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:01.989][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:01.989][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:01.996][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:02:01.998][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:02.000][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.001][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-01 16:02:02.003][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:02.004][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.005][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.006][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:02.006][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:02.006][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:02.006][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:02:02.006][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:02:02.007][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:02.008][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.009][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.010][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:02.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.012][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.013][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.014][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:02.015][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:02.016][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:02.017][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.018][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-01 16:02:02.019][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:02.020][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:02:02.021][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.022][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:02.023][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.024][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.025][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:02.026][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.027][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:02:02.027][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:02.028][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.029][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-01 16:02:02.030][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:02.031][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.032][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.033][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:02.033][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:02.033][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:02.033][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:02:02.033][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:02:02.034][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:02.035][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.036][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.036][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:02.037][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.038][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.039][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.040][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.041][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:02.042][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:02.042][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:02.043][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.044][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-01 16:02:02.046][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.047][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-01 16:02:02.048][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.049][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:02.050][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.051][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.051][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:02.052][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.053][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:02:02.054][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:02.055][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:02.056][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-01 16:02:02.057][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:02.058][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.059][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.060][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.061][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:02.061][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.062][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.063][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:02.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.066][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.066][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.067][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:02.068][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:02.069][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:02.070][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.071][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-01 16:02:02.073][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.074][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:02:02.074][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.075][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:02.076][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.077][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.078][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:02.079][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.080][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:02:02.081][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:02.082][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:02.083][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-01 16:02:02.083][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:02.084][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.085][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.086][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.087][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:02.103][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.106][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.108][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:02.109][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.109][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.110][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.111][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.112][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:02.113][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:02.114][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:02.114][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.116][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:02.116][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.137][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[2025-11-01 16:02:02.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.141][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[2025-11-01 16:02:02.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.182][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-01 16:02:02.183][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-01 16:02:02.184][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-01 16:02:02.186][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-01 16:02:02.187][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-01 16:02:02.188][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-01 16:02:02.189][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-01 16:02:02.190][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-01 16:02:02.192][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-01 16:02:02.193][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-01 16:02:02.199][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-01 16:02:02.200][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-01 16:02:02.201][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-01 16:02:02.203][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-01 16:02:02.204][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-01 16:02:02.205][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:02:02.206][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-01 16:02:02.207][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-01 16:02:02.209][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-01 16:02:02.210][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-01 16:02:02.211][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-01 16:02:02.212][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-01 16:02:02.213][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-01 16:02:02.215][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-01 16:02:02.216][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-01 16:02:02.217][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-01 16:02:02.218][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-01 16:02:02.220][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-01 16:02:02.221][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-01 16:02:02.222][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-01 16:02:02.223][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-01 16:02:02.224][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-01 16:02:02.226][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-01 16:02:02.227][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-01 16:02:02.228][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-01 16:02:02.229][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-01 16:02:02.230][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-01 16:02:02.232][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-01 16:02:02.233][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-01 16:02:02.234][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-01 16:02:02.235][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-01 16:02:02.236][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-01 16:02:02.238][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-01 16:02:02.239][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-01 16:02:02.240][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-01 16:02:02.241][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-01 16:02:02.243][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-01 16:02:02.244][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-01 16:02:02.245][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-01 16:02:02.246][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-01 16:02:02.248][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-01 16:02:02.249][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-01 16:02:02.250][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-01 16:02:02.251][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-01 16:02:02.252][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-01 16:02:02.254][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-01 16:02:02.255][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-01 16:02:02.256][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-01 16:02:02.257][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-01 16:02:02.259][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-01 16:02:02.260][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-01 16:02:02.261][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-01 16:02:02.262][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-01 16:02:02.263][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-01 16:02:02.265][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-01 16:02:02.266][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-01 16:02:02.267][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-01 16:02:02.268][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-01 16:02:02.270][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-01 16:02:02.271][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-01 16:02:02.272][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-01 16:02:02.273][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-01 16:02:02.274][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-01 16:02:02.276][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-01 16:02:02.277][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-01 16:02:02.278][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-01 16:02:02.279][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-01 16:02:02.280][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-01 16:02:02.282][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-01 16:02:02.283][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-01 16:02:02.288][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-01 16:02:02.290][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-01 16:02:02.291][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-01 16:02:02.292][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-01 16:02:02.294][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:02:02.295][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:02.296][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.297][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.320][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[2025-11-01 16:02:02.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.331][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[2025-11-01 16:02:02.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.342][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[2025-11-01 16:02:02.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.353][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[2025-11-01 16:02:02.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:02.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:02.392][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-11-01 16:02:02.394][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-11-01 16:02:02.396][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.396][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-11-01 16:02:02.397][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.398][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:02.399][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.400][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.401][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.402][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.403][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-11-01 16:02:02.404][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:02.404][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.405][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-11-01 16:02:02.406][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:02.407][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-11-01 16:02:02.407][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-11-01 16:02:02.408][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:02.409][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.410][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-01 16:02:02.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.411][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.412][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:02.413][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.414][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.415][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.416][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-11-01 16:02:02.416][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-11-01 16:02:02.416][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:02.417][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:02.418][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.419][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.420][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-11-01 16:02:02.422][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.423][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-11-01 16:02:02.423][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.424][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:02.425][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.426][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.427][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.428][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.429][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-01 16:02:02.430][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:02.431][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.431][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-11-01 16:02:02.432][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:02.433][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-11-01 16:02:02.433][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-11-01 16:02:02.433][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-11-01 16:02:02.433][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-11-01 16:02:02.433][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-11-01 16:02:02.433][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-11-01 16:02:02.434][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:02.435][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:02.436][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-01 16:02:02.437][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.438][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.438][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:02.439][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.440][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.441][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.442][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:02.442][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-01 16:02:02.443][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:02.443][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:02.444][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.445][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.446][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-11-01 16:02:02.448][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:02.449][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-11-01 16:02:02.450][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.451][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:02.452][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.452][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.453][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.454][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.455][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-01 16:02:02.456][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:02.457][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.458][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-11-01 16:02:02.459][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:02.459][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-01 16:02:02.459][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:02.459][self$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[2025-11-01 16:02:02.459][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:02.459][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:02.459][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:02.459][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:02.459][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:02.459][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:02.459][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:02.459][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-11-01 16:02:02.459][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:02.459][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:02.459][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:02.461][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:02.461][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:02.461][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:02.461][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:02.462][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-01 16:02:02.463][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.464][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.465][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:02.466][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.471][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.472][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.473][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:02.473][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-01 16:02:02.473][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-01 16:02:02.474][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:02.475][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:02.476][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.476][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-01 16:02:02.478][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-11-01 16:02:02.479][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.480][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-11-01 16:02:02.481][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.482][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:02.483][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.484][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.485][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.485][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.486][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-01 16:02:02.487][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:02.488][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.489][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-11-01 16:02:02.490][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:02.491][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-11-01 16:02:02.491][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-01 16:02:02.492][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:02.493][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:02.493][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-01 16:02:02.494][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.495][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.496][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:02.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:02.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:02.498][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:02.499][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:02.499][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-01 16:02:02.499][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-01 16:02:02.500][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:02.501][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:02.502][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:02.503][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-01 16:02:02.504][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-11-01 16:02:02.505][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-01 16:02:02.506][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:02:02.508][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-11-01 16:02:02.509][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-01 16:02:02.510][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-11-01 16:02:02.517][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2025-11-01 16:02:02.525][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2025-11-01 16:02:02.528][biodb::testThat]
biodb.INFO [2025-11-01 16:02:02.529][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-01 16:02:02.530][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:02.531][biodb::testThat]
biodb.TRACE[2025-11-01 16:02:02.533][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2025-11-01 16:02:02.534][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-11-01 16:02:02.537][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-11-01 16:02:02.539][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-01 16:02:02.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:02.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:02.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:02.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:02.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:02.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-01 16:02:02.552][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.553][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.555][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.559][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:02.560][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:02.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.562][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.563][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:02.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:02.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.573][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:02.574][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:02.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.576][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.577][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:02.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:02.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.580][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:02.581][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:02.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.583][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.584][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:02.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:02.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.587][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:02.588][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:02.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.590][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.591][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:02.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:02.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.595][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:02.596][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:02.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.597][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.599][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:02.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:02.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.602][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-11-01 16:02:02.603][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:02.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.605][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.606][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-11-01 16:02:02.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:02.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.610][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:02.611][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:02.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.612][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.613][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:02.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:02.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.617][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:02.618][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:02.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.620][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.621][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:02.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:02.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.625][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:02.626][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:02.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.628][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.629][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:02.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:02.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.633][ef$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:02.634][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:02.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.635][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.637][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:02.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:02.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.641][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-11-01 16:02:02.642][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:02.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.643][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-11-01 16:02:02.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:02.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.648][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:02.649][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:02.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.651][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.652][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:02.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:02.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.656][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:02.662][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:02.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.664][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.666][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:02.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:02.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.669][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-11-01 16:02:02.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:02.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.673][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:02.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:02.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.677][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:02.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:02.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.680][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-11-01 16:02:02.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:02.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.684][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:02.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:02.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.688][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:02.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:02.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.692][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-11-01 16:02:02.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:02.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.695][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:02.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:02.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.699][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:02.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:02.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.703][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-11-01 16:02:02.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:02.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.706][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:02.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:02.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.710][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:02.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:02.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.714][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-11-01 16:02:02.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:02.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.718][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:02.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:02.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.721][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:02.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:02.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.725][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:02.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:02.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.729][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:02.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:02.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.733][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:02.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:02.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.741][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:02.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:02.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:02:02.774][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2025-11-01 16:02:02.776][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:02.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:02.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.780][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:02.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:02.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.784][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:02.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:02.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.789][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:02.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:02.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.793][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:02.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:02.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.799][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:02.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:02.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.803][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:02.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:02.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.817][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:02.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:02.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.851][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:02.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:02.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.860][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:02.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:02.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.864][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:02.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:02.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.887][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.888][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.890][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:02.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:02.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.905][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-11-01 16:02:02.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:02.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:02.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:02.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:02.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:02.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.917][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-11-01 16:02:02.918][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:02.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.920][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.921][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-11-01 16:02:02.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:02.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-11-01 16:02:02.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:02.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:02.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:02.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:02.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:02.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.947][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-11-01 16:02:02.948][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:02.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.949][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-11-01 16:02:02.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:02.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.969][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:02.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:02.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.973][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:02.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:02.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.977][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:02.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:02.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.981][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:02.982][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:02.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.983][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.984][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:02.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:02.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:02.997][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:02.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:02.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:02.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.000][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:03.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:03.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.004][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:03.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:03.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.007][ef$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:03.008][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:03.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.010][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.011][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:03.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:03.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.022][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.026][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.030][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.033][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.034][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.036][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.037][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.049][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.052][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.061][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.064][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.065][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.067][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.068][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.079][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.083][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.086][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.090][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.091][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.093][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.093][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.105][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.108][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.112][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.115][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.116][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.118][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.119][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.130][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.134][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.137][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.141][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.142][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.143][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.148][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.160][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.164][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.167][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.171][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.172][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.174][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.175][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.186][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.190][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.193][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.197][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.198][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.199][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.200][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.212][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:03.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:03.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.215][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:03.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:03.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.219][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:03.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:03.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.223][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:03.224][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:03.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.225][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.226][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:03.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:03.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.246][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.250][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.253][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.254][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.256][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.268][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:03.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:03.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:03.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:03.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.276][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:03.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:03.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.279][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:03.280][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:03.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.282][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:03.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:03.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.297][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.299][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.300][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.305][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.306][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.308][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.314][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.315][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.318][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.324][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.325][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.326][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.331][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.332][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.334][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.343][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.345][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.347][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.352][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:03.353][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:03.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.355][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.360][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:03.361][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:03.362][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.362][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.367][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.368][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.370][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.375][ef$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:03.376][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:03.377][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.377][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.382][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:03.383][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:03.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.385][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.390][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:03.391][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:03.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.392][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.398][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:03.399][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:03.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.401][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.405][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.406][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.408][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.413][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.414][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.416][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.421][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2025-11-01 16:02:03.422][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-11-01 16:02:03.423][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-11-01 16:02:03.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-01 16:02:03.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:03.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:03.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:03.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:03.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:03.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-01 16:02:03.436][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.437][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.439][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.449][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.450][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.452][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.453][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.456][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.457][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.459][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.460][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.464][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.465][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.466][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.468][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.471][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.472][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.474][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.475][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.479][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.479][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.481][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.482][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.486][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-11-01 16:02:03.487][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:03.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.489][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.490][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-11-01 16:02:03.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:03.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.494][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:03.494][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:03.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.496][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.497][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:03.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:03.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.501][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:03.502][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:03.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.504][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:03.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:03.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.508][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.509][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.511][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.516][ef$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:03.517][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:03.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.519][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.520][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:03.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:03.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.523][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-11-01 16:02:03.524][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:03.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.526][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-11-01 16:02:03.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:03.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.535][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.536][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.538][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.539][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.543][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.544][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.545][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.546][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.550][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-11-01 16:02:03.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.553][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.557][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:03.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.560][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-11-01 16:02:03.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.564][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.567][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.571][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-11-01 16:02:03.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.574][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.578][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:03.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.581][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-11-01 16:02:03.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.585][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.589][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:03.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.592][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-11-01 16:02:03.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.596][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.599][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:03.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.603][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:03.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:03.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.606][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:03.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:03.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.610][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:03.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:03.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.622][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:03.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:03.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:02:03.646][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2025-11-01 16:02:03.648][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:03.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:03.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.652][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:03.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:03.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.655][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:03.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:03.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.659][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:03.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:03.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.662][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:03.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:03.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.666][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:03.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:03.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.669][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:03.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:03.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.682][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:03.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:03.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.717][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:03.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:03.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.721][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:03.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:03.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.724][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:03.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:03.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.745][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.745][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.747][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:03.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:03.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:03.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:03.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:03.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:03.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:03.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:03.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.771][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:03.772][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:03.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.773][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:03.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:03.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.785][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:03.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:03.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:03.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:03.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:03.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:03.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.802][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:03.803][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:03.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.804][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:03.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:03.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.817][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:03.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:03.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.820][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:03.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:03.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.824][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:03.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:03.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.827][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:03.828][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:03.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.830][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.831][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:03.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:03.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.842][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:03.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:03.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.846][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:03.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:03.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.850][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:03.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:03.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.853][ef$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:03.854][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:03.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.856][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.857][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:03.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:03.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.868][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.871][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.875][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.879][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.880][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.881][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.882][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:03.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.898][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.902][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.905][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.909][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.910][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.912][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.913][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:03.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.928][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.932][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.936][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.936][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.938][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.939][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:03.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.951][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:03.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:03.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.955][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:03.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:03.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.958][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:03.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:03.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.962][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:03.963][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:03.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.964][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.965][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:03.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:03.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.981][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.986][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.989][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.993][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.994][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.995][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:03.996][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:03.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:03.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.008][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:04.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:04.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.011][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:04.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:04.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.015][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:04.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:04.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.018][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:04.019][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:04.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.021][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.022][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:04.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:04.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.033][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:04.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:04.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.037][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:04.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:04.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.041][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:04.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:04.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.044][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:04.045][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:04.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.047][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.048][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:04.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:04.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.059][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:04.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:04.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.063][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:04.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:04.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.066][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:04.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:04.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.079][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:04.080][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:04.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.082][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.083][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:04.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:04.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.094][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:04.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:04.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.098][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:04.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:04.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.101][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:04.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:04.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.105][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:04.106][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:04.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.108][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.109][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:04.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:04.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.120][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:04.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:04.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.124][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:04.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:04.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.128][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:04.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:04.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.131][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:04.132][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:04.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.134][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.135][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:04.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:04.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.146][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:04.147][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:04.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.149][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.154][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:04.155][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-11-01 16:02:04.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.157][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.161][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:04.162][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-11-01 16:02:04.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.164][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.174][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:04.175][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-11-01 16:02:04.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.177][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.182][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:04.183][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:04.184][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.184][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.189][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:04.190][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:04.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.192][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.198][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:04.199][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:04.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.200][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.205][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:04.206][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:04.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.208][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.213][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:04.213][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:04.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.215][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.220][ef$get] Asked field names are: logp.
biodb.TRACE[2025-11-01 16:02:04.221][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-11-01 16:02:04.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.223][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.227][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:04.228][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:04.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.230][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.236][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:04.237][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:04.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.240][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.247][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:04.248][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:04.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.251][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.256][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:04.257][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-11-01 16:02:04.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.259][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.264][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:04.265][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-11-01 16:02:04.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.266][ef$get] fields variable is a list.
biodb.INFO [2025-11-01 16:02:04.279][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.280][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-01 16:02:04.281][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:04.282][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:04.284][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-11-01 16:02:04.289][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-11-01 16:02:04.290][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-01 16:02:04.291][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:04.292][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:04.293][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:04.294][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:04.294][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-11-01 16:02:04.307][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.308][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-01 16:02:04.309][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:04.310][biodb::testThat]
biodb.TRACE[2025-11-01 16:02:04.312][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:04.313][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:04.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.315][ef$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:02:04.316][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2025-11-01 16:02:04.326][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-11-01 16:02:04.327][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-11-01 16:02:04.328][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-01 16:02:04.329][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:04.330][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:04.331][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:04.332][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:04.333][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-11-01 16:02:04.347][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.348][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-01 16:02:04.349][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:04.349][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:04.357][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-11-01 16:02:04.358][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-11-01 16:02:04.359][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-01 16:02:04.360][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:04.361][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:04.362][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:04.363][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:04.364][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-11-01 16:02:04.383][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.384][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-01 16:02:04.384][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:04.385][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:04.389][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-11-01 16:02:04.390][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-11-01 16:02:04.391][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-01 16:02:04.392][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:04.393][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:04.394][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:04.395][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:04.396][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-11-01 16:02:04.408][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.409][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-01 16:02:04.410][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:04.411][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.424][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.425][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-01 16:02:04.426][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:04.427][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.440][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.441][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-01 16:02:04.441][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:04.442][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.455][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.456][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-01 16:02:04.457][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:04.458][biodb::testThat]
biodb.TRACE[2025-11-01 16:02:04.483][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:04.484][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:04.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.486][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.486][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:04.487][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:04.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.489][ef$get] fields variable is a list.
biodb.INFO [2025-11-01 16:02:04.491][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.492][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-11-01 16:02:04.492][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:04.493][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:04.501][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-11-01 16:02:04.502][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-11-01 16:02:04.503][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-01 16:02:04.504][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:04.505][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:04.506][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:04.507][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:04.508][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-11-01 16:02:04.521][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.522][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-11-01 16:02:04.522][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:04.523][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:04.526][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-11-01 16:02:04.527][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-11-01 16:02:04.528][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-01 16:02:04.529][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:04.530][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:04.531][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:04.532][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:04.533][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-11-01 16:02:04.546][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.551][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-11-01 16:02:04.552][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:04.553][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:04.556][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-11-01 16:02:04.557][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-11-01 16:02:04.559][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-01 16:02:04.560][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:04.561][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:04.562][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:04.562][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:04.563][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-11-01 16:02:04.576][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.577][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-11-01 16:02:04.578][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:04.579][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:04.582][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-11-01 16:02:04.582][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-11-01 16:02:04.584][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-01 16:02:04.585][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:04.586][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:04.587][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:04.588][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:04.589][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.TRACE[2025-11-01 16:02:04.601][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:04.602][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:04.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.604][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:04.605][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:04.606][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:04.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:04.607][ef$get] fields variable is a list.
biodb.INFO [2025-11-01 16:02:04.609][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.610][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-11-01 16:02:04.611][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:04.612][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:04.614][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-11-01 16:02:04.615][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-11-01 16:02:04.617][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-01 16:02:04.618][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:04.619][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:04.620][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:04.620][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:04.621][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-11-01 16:02:04.634][biodb::testThat]
biodb.INFO [2025-11-01 16:02:04.635][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-11-01 16:02:04.641][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:04.642][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:04.645][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-11-01 16:02:04.646][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-11-01 16:02:04.647][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-01 16:02:04.648][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:04.649][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:04.650][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:04.651][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:04.652][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-11-01 16:02:04.664][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-01 16:02:04.665][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2025-11-01 16:02:04.665][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-01 16:02:04.666][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:04.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:04.668][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.669][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-11-01 16:02:04.674][biodb::testContext]
biodb.INFO [2025-11-01 16:02:04.675][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:02:04.675][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2025-11-01 16:02:04.676][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:02:04.677][biodb::testContext]
biodb.INFO [2025-11-01 16:02:04.679][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:02:04.681][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-11-01 16:02:04.684][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:04.685][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-01 16:02:04.686][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-01 16:02:04.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.689][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-01 16:02:04.690][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-01 16:02:04.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.694][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-01 16:02:04.695][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-01 16:02:04.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.698][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-01 16:02:04.699][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-01 16:02:04.700][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-01 16:02:04.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.703][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-01 16:02:04.704][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-01 16:02:04.705][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-01 16:02:04.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.708][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-01 16:02:04.709][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-01 16:02:04.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.713][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-01 16:02:04.713][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-01 16:02:04.714][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-01 16:02:04.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.718][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-01 16:02:04.719][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-01 16:02:04.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.722][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-01 16:02:04.723][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-01 16:02:04.724][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-01 16:02:04.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.733][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:02:04.734][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-01 16:02:04.735][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-01 16:02:04.736][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-01 16:02:04.737][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-01 16:02:04.737][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-01 16:02:04.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.741][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-01 16:02:04.742][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-01 16:02:04.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.745][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-01 16:02:04.746][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-01 16:02:04.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.749][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-01 16:02:04.750][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-01 16:02:04.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.753][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-01 16:02:04.754][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-01 16:02:04.755][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-01 16:02:04.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.759][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:02:04.760][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-01 16:02:04.783][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-01 16:02:04.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.786][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-01 16:02:04.787][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-01 16:02:04.788][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-01 16:02:04.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.791][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-01 16:02:04.793][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:04.794][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-01 16:02:04.795][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.796][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:04.797][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.798][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:04.798][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:04.799][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:04.800][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:02:04.801][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:04.802][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.803][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-01 16:02:04.804][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:04.805][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:04.806][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.807][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:04.807][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:04.807][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:04.807][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:02:04.807][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:02:04.808][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:04.808][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:04.809][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:04.810][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:04.811][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:04.812][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:04.813][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:04.813][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:04.814][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:04.815][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:04.816][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:04.817][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:04.818][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-01 16:02:04.819][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:04.820][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:02:04.821][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.822][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:04.823][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.824][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:04.825][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:04.826][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:04.826][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:02:04.827][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:04.828][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.829][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-01 16:02:04.830][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:04.831][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:04.836][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.837][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:04.837][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:04.837][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:04.837][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:02:04.837][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:02:04.838][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:04.839][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:04.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:04.841][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:04.842][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:04.843][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:04.844][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:04.845][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:04.845][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:04.846][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:04.847][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:04.848][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:04.849][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-01 16:02:04.850][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.851][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-01 16:02:04.852][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.853][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:04.854][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.855][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:04.856][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:04.857][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:04.858][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:02:04.859][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:04.859][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:04.860][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-01 16:02:04.861][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:04.862][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:04.863][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.864][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:04.865][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:04.865][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:04.866][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:04.867][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:04.868][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:04.869][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:04.870][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:04.870][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:04.871][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:04.872][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:04.873][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:04.874][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:04.875][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-01 16:02:04.877][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.877][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:02:04.878][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.879][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:04.880][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.881][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:04.882][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:04.883][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:04.884][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:02:04.885][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:04.886][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:04.886][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-01 16:02:04.887][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:04.888][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:04.889][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:04.890][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:04.891][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:04.892][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:04.893][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:04.894][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:04.894][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:04.895][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:04.896][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:04.897][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:04.898][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:04.899][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:04.900][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:04.900][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:04.902][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:04.902][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.952][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[2025-11-01 16:02:04.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:04.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:04.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:04.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:04.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:04.973][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-01 16:02:04.974][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-01 16:02:04.976][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-01 16:02:04.977][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-01 16:02:04.978][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-01 16:02:04.979][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-01 16:02:04.980][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-01 16:02:04.982][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-01 16:02:04.983][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-01 16:02:04.984][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-01 16:02:04.985][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-01 16:02:04.987][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-01 16:02:04.988][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-01 16:02:04.989][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-01 16:02:04.990][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-01 16:02:04.992][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:02:04.993][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-01 16:02:04.994][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-01 16:02:04.995][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-01 16:02:04.996][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-01 16:02:05.002][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-01 16:02:05.004][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-01 16:02:05.005][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-01 16:02:05.007][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-01 16:02:05.008][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-01 16:02:05.009][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-01 16:02:05.010][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-01 16:02:05.011][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-01 16:02:05.013][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-01 16:02:05.014][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-01 16:02:05.015][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-01 16:02:05.016][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-01 16:02:05.017][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-01 16:02:05.019][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-01 16:02:05.020][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-01 16:02:05.021][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-01 16:02:05.022][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-01 16:02:05.023][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-01 16:02:05.025][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-01 16:02:05.026][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-01 16:02:05.027][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-01 16:02:05.028][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-01 16:02:05.030][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-01 16:02:05.031][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-01 16:02:05.032][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-01 16:02:05.033][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-01 16:02:05.034][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-01 16:02:05.036][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-01 16:02:05.037][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-01 16:02:05.038][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-01 16:02:05.039][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-01 16:02:05.040][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-01 16:02:05.042][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-01 16:02:05.043][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-01 16:02:05.044][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-01 16:02:05.046][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-01 16:02:05.047][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-01 16:02:05.048][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-01 16:02:05.049][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-01 16:02:05.051][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-01 16:02:05.052][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-01 16:02:05.053][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-01 16:02:05.054][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-01 16:02:05.056][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-01 16:02:05.057][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-01 16:02:05.058][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-01 16:02:05.059][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-01 16:02:05.060][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-01 16:02:05.062][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-01 16:02:05.063][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-01 16:02:05.064][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-01 16:02:05.065][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-01 16:02:05.067][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-01 16:02:05.068][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-01 16:02:05.069][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-01 16:02:05.070][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-01 16:02:05.071][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-01 16:02:05.073][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-01 16:02:05.074][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-01 16:02:05.075][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-01 16:02:05.076][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-01 16:02:05.083][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-01 16:02:05.084][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-01 16:02:05.085][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-01 16:02:05.087][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:02:05.088][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:05.089][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.090][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:05.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 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[2025-11-01 16:02:05.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:05.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.102][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[2025-11-01 16:02:05.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:05.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:05.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:05.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:05.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.130][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[2025-11-01 16:02:05.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:05.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.141][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[2025-11-01 16:02:05.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:05.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:05.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:05.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:05.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:05.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:05.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:05.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:05.186][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-11-01 16:02:05.188][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-11-01 16:02:05.190][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.191][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-11-01 16:02:05.191][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.192][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:05.193][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.194][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:05.195][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.196][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:05.197][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-11-01 16:02:05.197][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:05.198][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.199][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-11-01 16:02:05.200][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:05.201][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-11-01 16:02:05.201][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-11-01 16:02:05.202][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:05.203][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:05.204][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-01 16:02:05.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:05.205][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:05.206][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:05.207][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:05.208][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:05.209][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:05.210][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-11-01 16:02:05.210][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-11-01 16:02:05.211][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:05.211][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:05.212][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.213][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:05.214][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-11-01 16:02:05.216][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.217][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-11-01 16:02:05.218][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.219][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:05.219][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.220][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:05.221][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.222][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:05.223][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-01 16:02:05.224][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:05.225][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.226][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-11-01 16:02:05.226][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:05.227][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-11-01 16:02:05.227][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-11-01 16:02:05.227][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-11-01 16:02:05.227][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-11-01 16:02:05.227][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-11-01 16:02:05.227][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-11-01 16:02:05.228][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:05.229][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:05.230][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-01 16:02:05.231][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:05.232][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:05.233][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:05.234][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:05.234][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:05.235][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:05.236][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:05.236][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-01 16:02:05.237][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:05.238][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:05.239][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.239][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:05.245][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-11-01 16:02:05.247][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:05.248][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-11-01 16:02:05.249][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.250][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:05.251][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.252][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:05.253][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.253][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:05.254][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-01 16:02:05.255][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:05.256][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.257][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-11-01 16:02:05.258][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:05.259][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-01 16:02:05.259][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:05.259][self$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[2025-11-01 16:02:05.259][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:05.259][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:05.259][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:05.259][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:05.259][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:05.259][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:05.259][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:05.259][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-11-01 16:02:05.259][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:05.259][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:05.259][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-11-01 16:02:05.260][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:05.261][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:05.261][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:05.261][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:05.262][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-01 16:02:05.263][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:05.263][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:05.264][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:05.265][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:05.266][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:05.267][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:05.268][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:05.268][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-01 16:02:05.268][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-01 16:02:05.269][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:05.269][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:05.270][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.271][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-01 16:02:05.272][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-11-01 16:02:05.274][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.275][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-11-01 16:02:05.276][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.277][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:05.277][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.278][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:05.279][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.280][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:05.281][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-01 16:02:05.282][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:05.283][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.284][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-11-01 16:02:05.284][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:05.285][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-11-01 16:02:05.285][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-11-01 16:02:05.286][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:05.287][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:05.288][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-11-01 16:02:05.289][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:05.290][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:05.291][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:05.291][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:05.292][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:05.293][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:05.294][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:05.294][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-11-01 16:02:05.294][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-11-01 16:02:05.295][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:05.296][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:05.297][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:05.297][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-11-01 16:02:05.299][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-11-01 16:02:05.300][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-01 16:02:05.301][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:02:05.303][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-11-01 16:02:05.304][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-01 16:02:05.305][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-11-01 16:02:05.310][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2025-11-01 16:02:05.317][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2025-11-01 16:02:05.321][biodb::testThat]
biodb.INFO [2025-11-01 16:02:05.322][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-01 16:02:05.323][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:05.323][biodb::testThat]
biodb.TRACE[2025-11-01 16:02:05.462][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2025-11-01 16:02:05.463][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-11-01 16:02:05.466][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-11-01 16:02:05.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-01 16:02:05.468][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-01 16:02:05.482][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.483][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.485][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.489][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.490][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.492][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.493][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.497][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-01 16:02:05.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-01 16:02:05.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.500][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-01 16:02:05.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-01 16:02:05.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.507][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-01 16:02:05.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-01 16:02:05.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:02:05.532][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2025-11-01 16:02:05.534][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:05.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:05.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.537][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-11-01 16:02:05.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-11-01 16:02:05.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.541][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:05.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-11-01 16:02:05.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.544][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:05.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:05.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.548][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:05.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:05.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.551][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:05.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:05.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.555][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:05.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:05.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.566][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-01 16:02:05.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-01 16:02:05.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.601][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-01 16:02:05.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-01 16:02:05.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.605][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-01 16:02:05.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-01 16:02:05.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.609][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-01 16:02:05.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-11-01 16:02:05.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.632][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.633][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.634][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.635][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.651][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.655][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.659][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.663][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.664][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.666][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.667][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.679][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:05.680][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:05.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.682][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:05.688][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.689][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:05.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:05.691][ef$get] fields variable is a list.
biodb.INFO [2025-11-01 16:02:05.700][biodb::testThat]
biodb.INFO [2025-11-01 16:02:05.701][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-01 16:02:05.702][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:05.703][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:05.705][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-11-01 16:02:05.710][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-11-01 16:02:05.712][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-01 16:02:05.713][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:05.714][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:05.715][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:05.716][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:05.717][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-11-01 16:02:05.731][biodb::testThat]
biodb.INFO [2025-11-01 16:02:05.732][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-01 16:02:05.733][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:05.734][biodb::testThat]
biodb.INFO [2025-11-01 16:02:05.741][biodb::testThat]
biodb.INFO [2025-11-01 16:02:05.742][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-01 16:02:05.743][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:05.744][biodb::testThat]
biodb.WARN [2025-11-01 16:02:05.748][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-11-01 16:02:05.752][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-11-01 16:02:05.761][biodb::testThat]
biodb.INFO [2025-11-01 16:02:05.762][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-01 16:02:05.763][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:05.764][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:05.768][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-11-01 16:02:05.818][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-11-01 16:02:05.819][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-11-01 16:02:05.820][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-11-01 16:02:05.821][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:05.822][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-01 16:02:05.823][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-11-01 16:02:05.824][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-11-01 16:02:05.836][biodb::testThat]
biodb.INFO [2025-11-01 16:02:05.837][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-01 16:02:05.837][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:05.838][biodb::testThat]
biodb.INFO [2025-11-01 16:02:05.852][biodb::testThat]
biodb.INFO [2025-11-01 16:02:05.852][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-01 16:02:05.853][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:05.854][biodb::testThat]
biodb.INFO [2025-11-01 16:02:05.867][biodb::testThat]
biodb.INFO [2025-11-01 16:02:05.868][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-01 16:02:05.869][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:05.869][biodb::testThat]
biodb.INFO [2025-11-01 16:02:05.882][biodb::testThat]
biodb.INFO [2025-11-01 16:02:05.883][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-01 16:02:05.884][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:05.885][biodb::testThat]
biodb.INFO [2025-11-01 16:02:05.904][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-01 16:02:05.905][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2025-11-01 16:02:05.906][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-01 16:02:05.907][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:05.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:05.908][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:05.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:05.910][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:05.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ 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_1.14.0.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 ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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 ‘1.14.0’
** 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)