Back to Long Tests report for BioC 3.22

This page was generated on 2025-06-28 23:55 -0400 (Sat, 28 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4775
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4517
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4559
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/29HostnameOS / ArchCHECK
biodbNcbi 1.13.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-06-28 09:55 -0400 (Sat, 28 Jun 2025)
git_url: https://git.bioconductor.org/packages/biodbNcbi
git_branch: devel
git_last_commit: 79256f8
git_last_commit_date: 2025-04-15 12:47:49 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbNcbi on lconway

To the developers/maintainers of the biodbNcbi package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbNcbi
Version: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2025-06-28 16:01:10 -0400 (Sat, 28 Jun 2025)
EndedAt: 2025-06-28 16:01:59 -0400 (Sat, 28 Jun 2025)
EllapsedTime: 49.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNcbi.Rcheck
Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


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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)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNcbi")
Loading required package: biodbNcbi
biodb.INFO [2025-06-28 16:01:51.768][biodb::testContext]
biodb.INFO [2025-06-28 16:01:51.770][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-28 16:01:51.771][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2025-06-28 16:01:51.772][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-28 16:01:51.773][biodb::testContext]
biodb.INFO [2025-06-28 16:01:51.778][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-06-28 16:01:51.779][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-06-28 16:01:51.785][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-28 16:01:51.786][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-06-28 16:01:51.787][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-06-28 16:01:51.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.790][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-06-28 16:01:51.803][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-06-28 16:01:51.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.806][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-06-28 16:01:51.807][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-06-28 16:01:51.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.810][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-06-28 16:01:51.811][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-06-28 16:01:51.812][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-06-28 16:01:51.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.814][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-06-28 16:01:51.815][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-06-28 16:01:51.816][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-06-28 16:01:51.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.818][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-06-28 16:01:51.819][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-06-28 16:01:51.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.821][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-06-28 16:01:51.822][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-06-28 16:01:51.823][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-06-28 16:01:51.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.825][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-06-28 16:01:51.826][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-06-28 16:01:51.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.829][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-06-28 16:01:51.829][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-06-28 16:01:51.830][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-06-28 16:01:51.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.833][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-06-28 16:01:51.834][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-06-28 16:01:51.835][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-06-28 16:01:51.836][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-06-28 16:01:51.836][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-06-28 16:01:51.837][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-06-28 16:01:51.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.840][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-06-28 16:01:51.841][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-06-28 16:01:51.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.844][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-06-28 16:01:51.845][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-06-28 16:01:51.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.848][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-06-28 16:01:51.849][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-06-28 16:01:51.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.852][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-06-28 16:01:51.853][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-06-28 16:01:51.854][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-06-28 16:01:51.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.857][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-06-28 16:01:51.857][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-06-28 16:01:51.875][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-06-28 16:01:51.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.878][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-06-28 16:01:51.879][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-06-28 16:01:51.880][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-06-28 16:01:51.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:51.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:51.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:51.889][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-06-28 16:01:51.914][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:51.925][self$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[2025-06-28 16:01:51.926][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:51.927][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:51.928][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:51.929][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:51.930][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:51.930][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:51.931][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-28 16:01:51.932][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:51.933][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:51.933][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-06-28 16:01:51.934][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:51.935][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:51.936][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:51.937][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:51.937][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-28 16:01:51.937][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-28 16:01:51.937][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-28 16:01:51.937][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-28 16:01:51.937][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:51.938][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:51.939][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:51.940][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:51.941][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:51.941][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:51.942][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:51.943][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:51.943][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:51.944][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:51.945][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:51.945][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:51.946][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-06-28 16:01:51.948][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:51.948][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-06-28 16:01:51.949][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:51.950][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:51.951][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:51.951][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:51.952][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:51.953][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:51.953][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-28 16:01:51.954][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:51.955][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:51.956][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-06-28 16:01:51.957][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:51.957][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:51.958][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:51.959][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:51.959][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-28 16:01:51.959][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-28 16:01:51.959][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-28 16:01:51.959][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-28 16:01:51.960][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:51.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:51.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:51.962][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:51.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:51.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:51.964][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:51.965][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:51.966][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:51.966][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:51.967][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:51.968][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:51.969][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-06-28 16:01:51.970][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:51.971][self$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[2025-06-28 16:01:51.972][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:51.973][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:51.973][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:51.974][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:51.975][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:51.976][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:51.977][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-28 16:01:51.977][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:51.978][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:51.979][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-06-28 16:01:51.980][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:51.981][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:51.981][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:51.982][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:51.983][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:51.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:51.985][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:51.985][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:51.986][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:51.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:51.988][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:51.988][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:51.989][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:51.990][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:51.991][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:51.991][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:51.992][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-06-28 16:01:51.994][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:51.995][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-06-28 16:01:51.995][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:51.996][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:51.997][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:51.997][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:51.998][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:51.999][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:52.000][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-28 16:01:52.001][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:52.001][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:52.002][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-06-28 16:01:52.003][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:52.003][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:52.004][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.005][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:52.006][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:52.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:52.007][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:52.008][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:52.009][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:52.009][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:52.010][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:52.011][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:52.011][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:52.012][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:52.013][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:52.014][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:52.017][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-28 16:01:52.017][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.046][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[2025-06-28 16:01:52.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.076][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-06-28 16:01:52.079][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-06-28 16:01:52.080][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-06-28 16:01:52.081][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-06-28 16:01:52.082][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-06-28 16:01:52.083][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-06-28 16:01:52.084][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-06-28 16:01:52.085][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-06-28 16:01:52.086][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-06-28 16:01:52.087][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-06-28 16:01:52.088][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-06-28 16:01:52.089][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-06-28 16:01:52.090][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-06-28 16:01:52.091][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-06-28 16:01:52.092][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-06-28 16:01:52.093][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-06-28 16:01:52.094][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-06-28 16:01:52.095][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-06-28 16:01:52.096][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-06-28 16:01:52.097][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-06-28 16:01:52.099][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-06-28 16:01:52.100][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-06-28 16:01:52.101][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-06-28 16:01:52.102][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-06-28 16:01:52.103][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-06-28 16:01:52.104][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-06-28 16:01:52.105][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-06-28 16:01:52.106][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-06-28 16:01:52.107][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-06-28 16:01:52.109][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-06-28 16:01:52.110][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-06-28 16:01:52.110][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-06-28 16:01:52.111][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-06-28 16:01:52.112][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-06-28 16:01:52.113][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-06-28 16:01:52.114][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-06-28 16:01:52.115][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-06-28 16:01:52.116][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-06-28 16:01:52.117][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-06-28 16:01:52.118][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-06-28 16:01:52.119][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-06-28 16:01:52.120][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-06-28 16:01:52.121][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-06-28 16:01:52.122][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-06-28 16:01:52.123][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-06-28 16:01:52.124][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-06-28 16:01:52.125][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-06-28 16:01:52.126][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-06-28 16:01:52.127][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-06-28 16:01:52.128][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-06-28 16:01:52.129][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-06-28 16:01:52.130][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-06-28 16:01:52.131][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-06-28 16:01:52.132][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-06-28 16:01:52.133][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-06-28 16:01:52.134][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-06-28 16:01:52.135][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-06-28 16:01:52.136][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-06-28 16:01:52.138][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-06-28 16:01:52.139][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-06-28 16:01:52.140][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-06-28 16:01:52.141][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-06-28 16:01:52.142][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-06-28 16:01:52.143][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-06-28 16:01:52.144][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-06-28 16:01:52.145][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-06-28 16:01:52.146][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-06-28 16:01:52.147][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-06-28 16:01:52.148][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-06-28 16:01:52.149][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-06-28 16:01:52.150][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-06-28 16:01:52.151][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-06-28 16:01:52.153][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-06-28 16:01:52.154][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-06-28 16:01:52.155][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-06-28 16:01:52.160][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-06-28 16:01:52.161][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-06-28 16:01:52.162][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-06-28 16:01:52.163][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-06-28 16:01:52.164][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-06-28 16:01:52.165][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-06-28 16:01:52.166][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-06-28 16:01:52.167][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-06-28 16:01:52.172][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-06-28 16:01:52.173][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-06-28 16:01:52.175][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-28 16:01:52.176][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.178][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.228][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[2025-06-28 16:01:52.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.232][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[2025-06-28 16:01:52.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:52.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:52.257][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-06-28 16:01:52.265][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-06-28 16:01:52.266][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.267][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-06-28 16:01:52.268][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.268][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:52.269][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.270][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:52.271][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.272][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:52.272][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-06-28 16:01:52.273][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:52.274][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.275][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-06-28 16:01:52.275][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:52.276][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-06-28 16:01:52.276][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-06-28 16:01:52.277][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:52.278][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:52.279][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-06-28 16:01:52.280][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:52.280][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:52.281][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:52.282][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:52.283][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:52.283][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:52.284][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-06-28 16:01:52.284][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-06-28 16:01:52.285][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:52.286][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:52.286][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.287][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:52.288][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-06-28 16:01:52.293][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.294][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-06-28 16:01:52.295][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.296][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:52.297][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.297][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:52.298][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.299][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:52.300][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-28 16:01:52.300][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:52.301][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.302][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-06-28 16:01:52.303][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:52.303][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-06-28 16:01:52.303][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-06-28 16:01:52.303][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-06-28 16:01:52.303][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-06-28 16:01:52.303][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-06-28 16:01:52.303][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-06-28 16:01:52.304][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:52.305][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:52.306][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-06-28 16:01:52.307][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:52.307][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:52.308][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:52.309][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:52.310][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:52.310][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:52.311][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:52.311][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-06-28 16:01:52.312][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:52.313][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:52.314][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.314][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:52.315][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-06-28 16:01:52.317][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:52.317][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-06-28 16:01:52.318][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.319][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:52.320][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.321][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:52.321][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.322][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:52.323][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-28 16:01:52.324][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:52.324][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.325][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-06-28 16:01:52.326][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:52.327][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-06-28 16:01:52.327][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:52.327][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:52.327][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:52.327][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:52.327][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:52.327][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:52.327][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:52.327][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:52.327][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:52.327][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-06-28 16:01:52.327][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:52.327][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:52.327][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:52.328][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:52.329][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:52.329][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-28 16:01:52.329][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-28 16:01:52.329][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-06-28 16:01:52.330][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:52.331][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:52.332][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:52.332][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:52.333][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:52.334][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:52.335][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:52.335][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-06-28 16:01:52.335][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-06-28 16:01:52.336][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:52.336][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:52.337][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.338][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-06-28 16:01:52.339][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-06-28 16:01:52.340][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.341][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-06-28 16:01:52.341][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.342][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:52.343][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.343][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:52.344][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.345][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:52.346][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-28 16:01:52.347][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:52.348][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.349][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-06-28 16:01:52.349][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:52.350][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-06-28 16:01:52.350][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-06-28 16:01:52.351][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:52.351][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:52.352][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-06-28 16:01:52.353][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:52.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:52.354][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:52.355][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:52.356][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:52.356][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:52.357][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:52.357][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-06-28 16:01:52.357][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-06-28 16:01:52.358][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:52.358][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:52.359][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:52.360][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-06-28 16:01:52.365][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-06-28 16:01:52.366][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-06-28 16:01:52.367][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-06-28 16:01:52.369][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-06-28 16:01:52.370][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-06-28 16:01:52.371][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-06-28 16:01:52.389][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-06-28 16:01:52.403][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2025-06-28 16:01:52.410][biodb::testThat]
biodb.INFO [2025-06-28 16:01:52.411][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-06-28 16:01:52.412][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:52.413][biodb::testThat]
biodb.TRACE[2025-06-28 16:01:52.416][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2025-06-28 16:01:52.418][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-06-28 16:01:52.421][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-06-28 16:01:52.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-28 16:01:52.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-06-28 16:01:52.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.478][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-06-28 16:01:52.486][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.488][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.506][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-06-28 16:01:52.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.510][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.513][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.519][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-28 16:01:52.568][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2025-06-28 16:01:52.570][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.573][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.593][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-28 16:01:52.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-28 16:01:52.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.596][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-28 16:01:52.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-28 16:01:52.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.599][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-06-28 16:01:52.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-06-28 16:01:52.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.602][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-06-28 16:01:52.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-06-28 16:01:52.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.620][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.647][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.650][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.653][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.677][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.677][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.679][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.690][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-06-28 16:01:52.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.694][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.697][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.700][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-06-28 16:01:52.701][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.703][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.703][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-06-28 16:01:52.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.714][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.715][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.717][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.722][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.723][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.724][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.739][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2025-06-28 16:01:52.767][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-06-28 16:01:52.768][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-06-28 16:01:52.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-28 16:01:52.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:52.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:52.776][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:52.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:52.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:52.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-06-28 16:01:52.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.839][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-06-28 16:01:52.840][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.841][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.843][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-06-28 16:01:52.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.846][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.849][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.855][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-28 16:01:52.877][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2025-06-28 16:01:52.894][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.897][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:52.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.901][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-28 16:01:52.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-28 16:01:52.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.904][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-28 16:01:52.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-28 16:01:52.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.907][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-06-28 16:01:52.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-06-28 16:01:52.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.910][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-06-28 16:01:52.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-06-28 16:01:52.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.928][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.959][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.962][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.966][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:52.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.994][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.994][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.996][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:52.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:52.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:52.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:52.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:53.007][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-06-28 16:01:53.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:53.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:53.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:53.011][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:53.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:53.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:53.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:53.014][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:53.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:53.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:53.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:53.017][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-06-28 16:01:53.018][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:53.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:53.019][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:53.020][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-06-28 16:01:53.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:53.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:53.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:53.031][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:53.033][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:53.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:53.034][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:53.039][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:53.040][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:53.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:53.041][ef$get] fields variable is a list.
biodb.INFO [2025-06-28 16:01:53.049][biodb::testThat]
biodb.INFO [2025-06-28 16:01:53.050][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-06-28 16:01:53.055][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:53.056][biodb::testThat]
biodb.DEBUG[2025-06-28 16:01:53.057][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2025-06-28 16:01:53.060][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2025-06-28 16:01:53.062][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-06-28 16:01:53.063][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:53.064][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-06-28 16:01:53.065][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:53.066][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:53.100][biodb::testThat]
biodb.INFO [2025-06-28 16:01:53.101][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-06-28 16:01:53.102][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:53.102][biodb::testThat]
biodb.INFO [2025-06-28 16:01:53.108][biodb::testThat]
biodb.INFO [2025-06-28 16:01:53.109][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-06-28 16:01:53.110][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:53.110][biodb::testThat]
biodb.WARN [2025-06-28 16:01:53.126][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-06-28 16:01:53.141][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-06-28 16:01:53.149][biodb::testThat]
biodb.INFO [2025-06-28 16:01:53.150][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-06-28 16:01:53.150][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:53.151][biodb::testThat]
biodb.DEBUG[2025-06-28 16:01:53.170][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2025-06-28 16:01:53.203][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-06-28 16:01:53.225][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-06-28 16:01:53.226][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:53.227][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-06-28 16:01:53.228][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:53.228][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:53.259][biodb::testThat]
biodb.INFO [2025-06-28 16:01:53.260][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-06-28 16:01:53.261][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:53.262][biodb::testThat]
biodb.INFO [2025-06-28 16:01:53.273][biodb::testThat]
biodb.INFO [2025-06-28 16:01:53.274][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-06-28 16:01:53.275][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:53.276][biodb::testThat]
biodb.INFO [2025-06-28 16:01:53.282][biodb::testThat]
biodb.INFO [2025-06-28 16:01:53.283][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-06-28 16:01:53.284][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:53.285][biodb::testThat]
biodb.INFO [2025-06-28 16:01:53.296][biodb::testThat]
biodb.INFO [2025-06-28 16:01:53.297][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-06-28 16:01:53.298][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:53.298][biodb::testThat]
biodb.INFO [2025-06-28 16:01:53.304][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-06-28 16:01:53.305][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-06-28 16:01:53.305][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-06-28 16:01:53.306][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.307][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.309][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-06-28 16:01:53.317][biodb::testContext]
biodb.INFO [2025-06-28 16:01:53.318][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-28 16:01:53.319][biodb::testContext] Test context - Gene long tests
biodb.INFO [2025-06-28 16:01:53.320][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-28 16:01:53.321][biodb::testContext]
biodb.INFO [2025-06-28 16:01:53.322][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-06-28 16:01:53.324][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-06-28 16:01:53.326][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-28 16:01:53.327][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-06-28 16:01:53.328][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-06-28 16:01:53.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.331][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-06-28 16:01:53.331][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-06-28 16:01:53.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.334][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-06-28 16:01:53.335][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-06-28 16:01:53.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.338][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-06-28 16:01:53.338][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-06-28 16:01:53.339][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-06-28 16:01:53.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.342][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-06-28 16:01:53.343][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-06-28 16:01:53.343][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-06-28 16:01:53.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.346][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-06-28 16:01:53.347][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-06-28 16:01:53.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.350][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-06-28 16:01:53.351][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-06-28 16:01:53.352][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-06-28 16:01:53.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.359][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-06-28 16:01:53.360][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-06-28 16:01:53.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.363][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-06-28 16:01:53.364][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-06-28 16:01:53.365][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-06-28 16:01:53.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.368][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-06-28 16:01:53.369][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-06-28 16:01:53.370][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-06-28 16:01:53.371][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-06-28 16:01:53.371][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-06-28 16:01:53.372][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-06-28 16:01:53.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.375][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-06-28 16:01:53.376][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-06-28 16:01:53.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.378][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-06-28 16:01:53.379][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-06-28 16:01:53.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.382][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-06-28 16:01:53.383][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-06-28 16:01:53.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.385][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[2025-06-28 16:01:53.386][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-06-28 16:01:53.387][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-06-28 16:01:53.387][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-06-28 16:01:53.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.390][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-06-28 16:01:53.391][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-06-28 16:01:53.409][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-06-28 16:01:53.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.416][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-06-28 16:01:53.417][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-06-28 16:01:53.418][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-06-28 16:01:53.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.451][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-06-28 16:01:53.453][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.454][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-06-28 16:01:53.455][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.455][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:53.456][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.457][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.458][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.459][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.459][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-28 16:01:53.460][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:53.461][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.461][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-06-28 16:01:53.462][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:53.463][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.464][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.465][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:53.465][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-28 16:01:53.465][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-28 16:01:53.465][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-28 16:01:53.465][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-28 16:01:53.465][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:53.466][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.467][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.467][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:53.468][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.470][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.470][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.471][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:53.472][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:53.472][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.473][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.474][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-06-28 16:01:53.475][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.476][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-06-28 16:01:53.477][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.478][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:53.479][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.479][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.480][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.481][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.481][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-28 16:01:53.482][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:53.483][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.483][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-06-28 16:01:53.484][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:53.485][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.486][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.486][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:53.486][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-28 16:01:53.486][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-28 16:01:53.486][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-28 16:01:53.486][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-28 16:01:53.487][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:53.488][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.488][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.489][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:53.490][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.491][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.491][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.492][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.493][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:53.493][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:53.494][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.495][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.496][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-06-28 16:01:53.497][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.498][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-06-28 16:01:53.499][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.499][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:53.500][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.501][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.502][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.502][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.503][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-28 16:01:53.504][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:53.505][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.505][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-06-28 16:01:53.506][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:53.507][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.508][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.508][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.513][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:53.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.514][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.515][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:53.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.517][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.518][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.519][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:53.519][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:53.520][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.521][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.522][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-06-28 16:01:53.523][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.524][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-06-28 16:01:53.524][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.525][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:53.526][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.526][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.527][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.528][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.529][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-28 16:01:53.529][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:53.530][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.531][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-06-28 16:01:53.532][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:53.532][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.533][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.534][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.535][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:53.536][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.536][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.537][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:53.538][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.538][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.539][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.540][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.541][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:53.541][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:53.542][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.543][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.544][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-28 16:01:53.545][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.601][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-06-28 16:01:53.602][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-06-28 16:01:53.603][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-06-28 16:01:53.604][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-06-28 16:01:53.606][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-06-28 16:01:53.607][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-06-28 16:01:53.608][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-06-28 16:01:53.609][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-06-28 16:01:53.610][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-06-28 16:01:53.611][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-06-28 16:01:53.616][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-06-28 16:01:53.617][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-06-28 16:01:53.618][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-06-28 16:01:53.620][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-06-28 16:01:53.621][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-06-28 16:01:53.622][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-06-28 16:01:53.623][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-06-28 16:01:53.624][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-06-28 16:01:53.625][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-06-28 16:01:53.626][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-06-28 16:01:53.627][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-06-28 16:01:53.628][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-06-28 16:01:53.630][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-06-28 16:01:53.631][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-06-28 16:01:53.632][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-06-28 16:01:53.633][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-06-28 16:01:53.634][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-06-28 16:01:53.635][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-06-28 16:01:53.637][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-06-28 16:01:53.638][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-06-28 16:01:53.639][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-06-28 16:01:53.640][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-06-28 16:01:53.641][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-06-28 16:01:53.643][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-06-28 16:01:53.644][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-06-28 16:01:53.645][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-06-28 16:01:53.646][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-06-28 16:01:53.647][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-06-28 16:01:53.648][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-06-28 16:01:53.650][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-06-28 16:01:53.651][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-06-28 16:01:53.652][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-06-28 16:01:53.653][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-06-28 16:01:53.655][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-06-28 16:01:53.656][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-06-28 16:01:53.657][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-06-28 16:01:53.658][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-06-28 16:01:53.660][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-06-28 16:01:53.661][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-06-28 16:01:53.662][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-06-28 16:01:53.664][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-06-28 16:01:53.666][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-06-28 16:01:53.667][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-06-28 16:01:53.669][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-06-28 16:01:53.672][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-06-28 16:01:53.674][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-06-28 16:01:53.677][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-06-28 16:01:53.679][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-06-28 16:01:53.681][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-06-28 16:01:53.683][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-06-28 16:01:53.685][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-06-28 16:01:53.688][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-06-28 16:01:53.690][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-06-28 16:01:53.692][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-06-28 16:01:53.694][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-06-28 16:01:53.696][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-06-28 16:01:53.698][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-06-28 16:01:53.700][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-06-28 16:01:53.702][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-06-28 16:01:53.703][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-06-28 16:01:53.705][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-06-28 16:01:53.706][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-06-28 16:01:53.708][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-06-28 16:01:53.710][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-06-28 16:01:53.712][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-06-28 16:01:53.713][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-06-28 16:01:53.714][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-06-28 16:01:53.716][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-06-28 16:01:53.717][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-06-28 16:01:53.718][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-06-28 16:01:53.719][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-06-28 16:01:53.720][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-06-28 16:01:53.722][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-06-28 16:01:53.723][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-06-28 16:01:53.725][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-06-28 16:01:53.726][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-28 16:01:53.726][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.728][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.740][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[2025-06-28 16:01:53.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:53.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:53.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:53.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:53.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:53.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:53.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:53.813][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-06-28 16:01:53.814][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-06-28 16:01:53.816][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.817][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-06-28 16:01:53.818][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.818][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:53.819][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.820][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.820][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.821][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.822][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-06-28 16:01:53.822][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:53.823][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.824][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-06-28 16:01:53.825][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:53.825][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-06-28 16:01:53.825][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-06-28 16:01:53.826][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.827][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.827][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-06-28 16:01:53.828][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.829][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.829][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:53.830][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.831][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.832][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.833][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-06-28 16:01:53.833][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-06-28 16:01:53.834][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:53.834][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:53.835][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.836][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.837][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-06-28 16:01:53.838][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.839][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-06-28 16:01:53.839][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.840][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:53.841][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.842][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.842][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.843][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.844][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-28 16:01:53.845][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:53.849][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.850][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-06-28 16:01:53.851][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:53.852][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-06-28 16:01:53.852][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-06-28 16:01:53.852][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-06-28 16:01:53.852][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-06-28 16:01:53.852][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-06-28 16:01:53.852][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-06-28 16:01:53.852][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.853][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:53.854][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-06-28 16:01:53.854][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.855][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.856][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:53.857][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.857][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.858][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.859][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:53.859][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-06-28 16:01:53.859][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:53.860][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:53.861][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.862][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.862][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-06-28 16:01:53.864][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.865][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-06-28 16:01:53.865][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.866][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:53.867][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.867][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.868][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.869][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.870][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-28 16:01:53.870][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:53.871][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.872][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-06-28 16:01:53.873][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:53.874][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-06-28 16:01:53.874][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:53.874][self$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[2025-06-28 16:01:53.874][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:53.874][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:53.874][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:53.874][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:53.874][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:53.874][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:53.874][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:53.874][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-06-28 16:01:53.874][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:53.874][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:53.874][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:53.875][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.876][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:53.876][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-28 16:01:53.876][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-28 16:01:53.876][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-06-28 16:01:53.877][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.878][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.878][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:53.879][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.880][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.881][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.881][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:53.881][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-06-28 16:01:53.881][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-06-28 16:01:53.882][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:53.883][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:53.884][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.884][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-06-28 16:01:53.885][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-06-28 16:01:53.887][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.887][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-06-28 16:01:53.888][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.889][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:53.890][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.891][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.891][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.892][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.893][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-28 16:01:53.894][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:53.894][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.895][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-06-28 16:01:53.896][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:53.897][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-06-28 16:01:53.897][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-06-28 16:01:53.898][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:53.898][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:53.899][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-06-28 16:01:53.900][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.901][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.902][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:53.902][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:53.903][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:53.904][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:53.904][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:53.904][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-06-28 16:01:53.904][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-06-28 16:01:53.905][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:53.906][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:53.906][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:53.907][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-06-28 16:01:53.908][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-06-28 16:01:53.909][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-06-28 16:01:53.911][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-06-28 16:01:53.912][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-06-28 16:01:53.913][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-06-28 16:01:53.914][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-06-28 16:01:53.920][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2025-06-28 16:01:53.986][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2025-06-28 16:01:53.989][biodb::testThat]
biodb.INFO [2025-06-28 16:01:53.990][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-06-28 16:01:53.990][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:53.991][biodb::testThat]
biodb.TRACE[2025-06-28 16:01:53.996][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2025-06-28 16:01:53.997][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-06-28 16:01:53.999][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-06-28 16:01:54.001][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-28 16:01:54.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.006][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.008][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-06-28 16:01:54.018][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:54.019][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:54.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.021][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:54.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:54.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.026][ef$get] Asked field names are: description.
biodb.TRACE[2025-06-28 16:01:54.027][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-06-28 16:01:54.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.028][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.029][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-06-28 16:01:54.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-06-28 16:01:54.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.033][ef$get] Asked field names are: location.
biodb.TRACE[2025-06-28 16:01:54.034][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-06-28 16:01:54.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.035][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.036][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-06-28 16:01:54.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-06-28 16:01:54.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.040][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-06-28 16:01:54.040][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-06-28 16:01:54.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.042][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.043][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-06-28 16:01:54.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-06-28 16:01:54.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.046][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-06-28 16:01:54.047][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:54.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.053][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.055][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-06-28 16:01:54.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:54.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.057][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-06-28 16:01:54.058][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-06-28 16:01:54.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.060][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.062][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-06-28 16:01:54.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-06-28 16:01:54.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.068][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:54.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:54.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.072][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-06-28 16:01:54.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-06-28 16:01:54.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.074][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-06-28 16:01:54.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-06-28 16:01:54.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:54.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:54.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.081][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-06-28 16:01:54.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-06-28 16:01:54.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:54.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:54.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:54.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:54.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:54.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:54.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:54.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:54.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:54.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:54.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:54.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:54.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-28 16:01:54.102][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2025-06-28 16:01:54.103][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:54.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:54.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.106][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:54.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:54.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.109][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:54.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:54.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.112][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:54.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:54.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:54.115][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:54.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:54.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-28 16:01:54.118][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-06-28 16:01:54.145][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-06-28 16:01:54.155][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2025-06-28 16:01:54.156][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2025-06-28 16:01:54.159][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-06-28 16:01:54.160][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-06-28 16:01:54.161][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:54.162][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-06-28 16:01:54.162][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:54.163][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:54.175][biodb::testThat]
biodb.INFO [2025-06-28 16:01:54.176][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-06-28 16:01:54.177][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:54.177][biodb::testThat]
biodb.DEBUG[2025-06-28 16:01:54.179][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2025-06-28 16:01:54.180][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2025-06-28 16:01:54.181][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-06-28 16:01:54.182][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:54.183][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:54.184][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:54.185][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:54.186][private$retrieveContents] Get entry content(s) for 8 id(s)...
biodb.INFO [2025-06-28 16:01:54.200][biodb::testThat]
biodb.INFO [2025-06-28 16:01:54.200][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-06-28 16:01:54.201][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:54.202][biodb::testThat]
biodb.TRACE[2025-06-28 16:01:54.205][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:54.205][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:54.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:54.207][ef$get] fields variable is a list.
biodb.DEBUG[2025-06-28 16:01:54.208][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2025-06-28 16:01:54.216][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-06-28 16:01:54.217][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-06-28 16:01:54.218][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-06-28 16:01:54.219][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:54.219][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:54.220][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:54.221][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:54.238][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-06-28 16:01:54.267][biodb::testThat]
biodb.INFO [2025-06-28 16:01:54.268][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-06-28 16:01:54.269][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:54.270][biodb::testThat]
biodb.DEBUG[2025-06-28 16:01:54.279][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-06-28 16:01:54.280][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-06-28 16:01:54.281][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-06-28 16:01:54.283][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:54.284][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:54.285][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:54.286][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:54.287][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-06-28 16:01:54.301][biodb::testThat]
biodb.INFO [2025-06-28 16:01:54.302][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-06-28 16:01:54.303][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:54.304][biodb::testThat]
biodb.DEBUG[2025-06-28 16:01:54.307][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-06-28 16:01:54.308][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-06-28 16:01:54.309][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-06-28 16:01:54.310][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:54.311][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:54.312][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:54.313][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:54.314][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-06-28 16:01:54.329][biodb::testThat]
biodb.INFO [2025-06-28 16:01:54.330][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-06-28 16:01:54.331][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:54.332][biodb::testThat]
biodb.INFO [2025-06-28 16:01:54.350][biodb::testThat]
biodb.INFO [2025-06-28 16:01:54.351][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-06-28 16:01:54.352][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:54.353][biodb::testThat]
biodb.INFO [2025-06-28 16:01:54.360][biodb::testThat]
biodb.INFO [2025-06-28 16:01:54.361][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-06-28 16:01:54.362][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:54.363][biodb::testThat]
biodb.INFO [2025-06-28 16:01:54.375][biodb::testThat]
biodb.INFO [2025-06-28 16:01:54.376][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-06-28 16:01:54.377][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:54.377][biodb::testThat]
biodb.INFO [2025-06-28 16:01:54.383][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-06-28 16:01:54.384][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2025-06-28 16:01:54.385][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-06-28 16:01:54.386][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-06-28 16:01:54.387][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.388][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.390][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-06-28 16:01:54.394][biodb::testContext]
biodb.INFO [2025-06-28 16:01:54.394][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-28 16:01:54.395][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2025-06-28 16:01:54.396][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-28 16:01:54.397][biodb::testContext]
biodb.INFO [2025-06-28 16:01:54.398][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-06-28 16:01:54.400][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-06-28 16:01:54.403][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-28 16:01:54.404][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-06-28 16:01:54.405][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-06-28 16:01:54.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.408][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-06-28 16:01:54.408][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-06-28 16:01:54.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.411][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-06-28 16:01:54.412][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-06-28 16:01:54.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.416][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-06-28 16:01:54.416][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-06-28 16:01:54.417][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-06-28 16:01:54.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.420][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-06-28 16:01:54.421][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-06-28 16:01:54.422][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-06-28 16:01:54.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.425][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-06-28 16:01:54.426][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-06-28 16:01:54.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.429][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-06-28 16:01:54.430][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-06-28 16:01:54.431][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-06-28 16:01:54.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.434][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-06-28 16:01:54.435][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-06-28 16:01:54.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.438][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-06-28 16:01:54.439][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-06-28 16:01:54.440][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-06-28 16:01:54.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.449][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-06-28 16:01:54.450][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-06-28 16:01:54.451][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-06-28 16:01:54.452][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-06-28 16:01:54.453][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-06-28 16:01:54.454][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-06-28 16:01:54.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.458][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-06-28 16:01:54.459][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-06-28 16:01:54.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.461][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[2025-06-28 16:01:54.463][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-06-28 16:01:54.465][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-06-28 16:01:54.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.469][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-06-28 16:01:54.470][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-06-28 16:01:54.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.473][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[2025-06-28 16:01:54.475][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-06-28 16:01:54.476][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-06-28 16:01:54.477][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-06-28 16:01:54.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.481][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-06-28 16:01:54.483][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-06-28 16:01:54.507][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-06-28 16:01:54.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.513][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-06-28 16:01:54.514][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-06-28 16:01:54.515][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-06-28 16:01:54.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.520][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-06-28 16:01:54.521][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.522][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-06-28 16:01:54.523][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.524][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:54.525][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.526][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.527][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.528][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.529][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-28 16:01:54.529][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:54.530][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.531][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-06-28 16:01:54.532][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:54.533][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.534][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.535][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:54.535][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-28 16:01:54.535][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-28 16:01:54.535][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-28 16:01:54.535][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-28 16:01:54.536][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:54.536][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.537][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.538][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:54.539][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.541][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.542][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.543][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:54.544][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:54.544][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.545][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.546][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-06-28 16:01:54.548][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.549][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-06-28 16:01:54.549][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.550][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:54.551][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.552][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.553][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.554][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.554][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-28 16:01:54.555][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:54.556][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.557][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-06-28 16:01:54.558][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:54.559][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.559][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.560][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:54.560][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-28 16:01:54.560][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-28 16:01:54.560][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-28 16:01:54.560][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-28 16:01:54.561][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:54.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.564][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:54.564][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.565][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.566][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.567][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.568][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:54.568][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:54.569][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.570][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.571][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-06-28 16:01:54.573][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.574][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-06-28 16:01:54.575][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.576][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:54.577][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.578][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.578][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.579][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.580][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-28 16:01:54.581][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:54.582][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.583][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-06-28 16:01:54.584][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:54.585][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.593][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.594][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.596][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:54.597][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.598][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.599][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:54.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.603][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.604][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.605][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:54.607][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:54.608][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.609][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.610][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-06-28 16:01:54.612][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.613][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-06-28 16:01:54.614][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.615][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:54.616][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.617][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.618][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.620][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.621][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-28 16:01:54.622][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:54.624][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.625][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-06-28 16:01:54.626][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:54.628][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.629][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.630][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.631][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:54.632][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.633][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.634][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:54.635][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.635][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.636][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.637][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.638][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:54.638][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:54.639][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.640][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.642][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-28 16:01:54.643][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.693][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[2025-06-28 16:01:54.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.705][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-06-28 16:01:54.706][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-06-28 16:01:54.707][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-06-28 16:01:54.708][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-06-28 16:01:54.709][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-06-28 16:01:54.710][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-06-28 16:01:54.711][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-06-28 16:01:54.712][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-06-28 16:01:54.714][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-06-28 16:01:54.715][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-06-28 16:01:54.716][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-06-28 16:01:54.717][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-06-28 16:01:54.718][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-06-28 16:01:54.719][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-06-28 16:01:54.720][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-06-28 16:01:54.721][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-06-28 16:01:54.722][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-06-28 16:01:54.723][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-06-28 16:01:54.724][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-06-28 16:01:54.726][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-06-28 16:01:54.727][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-06-28 16:01:54.728][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-06-28 16:01:54.729][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-06-28 16:01:54.730][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-06-28 16:01:54.731][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-06-28 16:01:54.732][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-06-28 16:01:54.733][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-06-28 16:01:54.734][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-06-28 16:01:54.735][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-06-28 16:01:54.736][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-06-28 16:01:54.737][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-06-28 16:01:54.738][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-06-28 16:01:54.740][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-06-28 16:01:54.741][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-06-28 16:01:54.742][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-06-28 16:01:54.743][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-06-28 16:01:54.744][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-06-28 16:01:54.745][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-06-28 16:01:54.746][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-06-28 16:01:54.747][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-06-28 16:01:54.748][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-06-28 16:01:54.749][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-06-28 16:01:54.750][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-06-28 16:01:54.751][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-06-28 16:01:54.752][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-06-28 16:01:54.753][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-06-28 16:01:54.755][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-06-28 16:01:54.756][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-06-28 16:01:54.757][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-06-28 16:01:54.758][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-06-28 16:01:54.759][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-06-28 16:01:54.760][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-06-28 16:01:54.761][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-06-28 16:01:54.762][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-06-28 16:01:54.763][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-06-28 16:01:54.764][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-06-28 16:01:54.765][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-06-28 16:01:54.766][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-06-28 16:01:54.767][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-06-28 16:01:54.768][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-06-28 16:01:54.769][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-06-28 16:01:54.770][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-06-28 16:01:54.771][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-06-28 16:01:54.772][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-06-28 16:01:54.773][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-06-28 16:01:54.774][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-06-28 16:01:54.775][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-06-28 16:01:54.776][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-06-28 16:01:54.777][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-06-28 16:01:54.778][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-06-28 16:01:54.779][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-06-28 16:01:54.780][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-06-28 16:01:54.781][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-06-28 16:01:54.782][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-06-28 16:01:54.783][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-06-28 16:01:54.785][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-06-28 16:01:54.790][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-06-28 16:01:54.791][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-06-28 16:01:54.792][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-06-28 16:01:54.793][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-06-28 16:01:54.794][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-06-28 16:01:54.795][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-06-28 16:01:54.796][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-06-28 16:01:54.798][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-06-28 16:01:54.799][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-06-28 16:01:54.800][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-28 16:01:54.801][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.802][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.864][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[2025-06-28 16:01:54.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:54.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:54.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:54.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:54.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:54.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:54.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:54.884][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-06-28 16:01:54.886][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-06-28 16:01:54.887][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.888][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-06-28 16:01:54.889][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.890][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:54.890][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.891][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.892][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.892][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.893][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-06-28 16:01:54.894][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:54.895][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.895][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-06-28 16:01:54.896][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:54.897][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-06-28 16:01:54.897][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-06-28 16:01:54.898][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.899][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.900][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-06-28 16:01:54.900][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.901][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.902][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:54.902][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.903][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.904][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.905][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-06-28 16:01:54.905][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-06-28 16:01:54.905][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:54.906][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:54.907][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.907][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.908][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-06-28 16:01:54.910][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.910][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-06-28 16:01:54.911][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.912][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:54.913][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.913][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.914][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.915][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.915][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-28 16:01:54.916][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:54.917][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.917][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-06-28 16:01:54.918][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:54.919][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-06-28 16:01:54.919][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-06-28 16:01:54.919][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-06-28 16:01:54.919][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-06-28 16:01:54.919][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-06-28 16:01:54.919][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-06-28 16:01:54.920][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.921][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:54.921][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-06-28 16:01:54.922][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.923][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.923][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:54.924][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.925][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.925][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.926][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:54.926][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-06-28 16:01:54.927][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:54.927][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:54.928][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.929][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.930][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-06-28 16:01:54.931][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.932][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-06-28 16:01:54.932][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.933][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:54.934][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.934][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.935][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.936][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.937][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-28 16:01:54.938][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:54.938][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.939][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-06-28 16:01:54.940][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:54.941][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-06-28 16:01:54.941][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:54.941][self$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[2025-06-28 16:01:54.941][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:54.941][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:54.941][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:54.941][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:54.941][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:54.941][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:54.941][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:54.941][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-06-28 16:01:54.941][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:54.941][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:54.941][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:54.941][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.942][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:54.942][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-28 16:01:54.942][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-28 16:01:54.943][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-06-28 16:01:54.944][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.944][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.945][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:54.946][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.946][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.947][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.948][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:54.948][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-06-28 16:01:54.948][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-06-28 16:01:54.949][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:54.950][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:54.950][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.951][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-06-28 16:01:54.952][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-06-28 16:01:54.953][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.954][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-06-28 16:01:54.955][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.956][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:54.957][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.957][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.958][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.959][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.960][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-28 16:01:54.961][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:54.961][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.962][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-06-28 16:01:54.967][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:54.968][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-06-28 16:01:54.968][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-06-28 16:01:54.969][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:54.969][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:54.970][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-06-28 16:01:54.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.972][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:54.973][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:54.974][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:54.974][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:54.975][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:54.975][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-06-28 16:01:54.975][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-06-28 16:01:54.976][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:54.977][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:54.977][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:54.978][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-06-28 16:01:54.979][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-06-28 16:01:54.980][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-06-28 16:01:54.982][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-06-28 16:01:54.983][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-06-28 16:01:54.984][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-06-28 16:01:54.985][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-06-28 16:01:54.991][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2025-06-28 16:01:54.997][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2025-06-28 16:01:55.001][biodb::testThat]
biodb.INFO [2025-06-28 16:01:55.002][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-06-28 16:01:55.002][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:55.003][biodb::testThat]
biodb.TRACE[2025-06-28 16:01:55.005][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2025-06-28 16:01:55.006][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-06-28 16:01:55.009][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-06-28 16:01:55.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-28 16:01:55.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:55.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:55.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:55.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:55.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:55.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-06-28 16:01:55.022][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.023][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.024][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.029][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.029][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.031][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.032][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.035][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.036][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.038][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.039][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.042][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.043][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.044][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.045][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.049][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.049][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.051][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.052][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.055][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.056][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.058][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.059][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.062][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-06-28 16:01:55.080][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:55.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.082][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.083][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-06-28 16:01:55.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:55.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.086][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:55.087][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:55.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.088][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.089][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:55.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:55.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.092][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:55.093][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:55.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.094][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.096][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:55.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:55.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.099][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.100][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.101][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.106][ef$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:55.106][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:55.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.108][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.109][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:55.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:55.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.112][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-06-28 16:01:55.113][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:55.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.115][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-06-28 16:01:55.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:55.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.119][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.120][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.121][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.122][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.126][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.126][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.128][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.129][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.132][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-06-28 16:01:55.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.135][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.138][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.141][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-06-28 16:01:55.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.145][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.148][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.151][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-06-28 16:01:55.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.154][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.157][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.160][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-06-28 16:01:55.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.164][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.171][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.175][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-06-28 16:01:55.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.179][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.182][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.185][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:55.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:55.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.188][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.191][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.197][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-28 16:01:55.217][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2025-06-28 16:01:55.219][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:55.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:55.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.222][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:55.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:55.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.225][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:55.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:55.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.228][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-28 16:01:55.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-28 16:01:55.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.230][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-28 16:01:55.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-28 16:01:55.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.233][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-06-28 16:01:55.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-06-28 16:01:55.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.236][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-06-28 16:01:55.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-06-28 16:01:55.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.247][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.277][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.280][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.283][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.301][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.302][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.303][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.314][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-06-28 16:01:55.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:55.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:55.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:55.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:55.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:55.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.323][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-06-28 16:01:55.324][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:55.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.325][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.326][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-06-28 16:01:55.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:55.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-06-28 16:01:55.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:55.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:55.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:55.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:55.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:55.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.345][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-06-28 16:01:55.346][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:55.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.352][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-06-28 16:01:55.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:55.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.363][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:55.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:55.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.366][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:55.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:55.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.369][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:55.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:55.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.372][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:55.373][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:55.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.374][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.375][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:55.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:55.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.385][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:55.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:55.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.388][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:55.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:55.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.391][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:55.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:55.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.393][ef$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:55.394][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:55.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.396][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.396][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:55.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:55.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.405][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.408][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.411][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.414][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.415][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.416][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.417][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.427][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.430][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.433][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.436][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.437][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.443][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.444][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.454][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.457][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.460][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.463][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.464][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.465][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.466][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.476][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.479][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.482][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.485][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.486][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.487][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.488][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.501][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.504][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.507][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.508][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.509][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.510][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.520][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.523][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.526][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.530][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.530][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.537][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.538][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.548][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.552][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.555][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.558][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.558][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.560][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.561][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.570][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:55.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:55.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:55.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:55.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:55.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:55.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.579][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:55.580][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:55.581][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.582][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:55.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:55.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.601][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.602][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.604][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.615][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:55.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:55.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:55.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:55.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.621][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:55.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:55.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.624][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:55.629][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:55.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.630][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.631][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:55.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:55.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.641][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.642][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.643][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.648][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.648][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.650][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.654][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.655][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.656][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.660][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.661][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.663][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.667][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.668][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.669][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.673][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.674][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.676][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.680][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:55.681][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:55.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.682][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.686][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:55.687][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:55.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.689][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.693][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.693][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.695][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.699][ef$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:55.700][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:55.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.701][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.706][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:55.706][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:55.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.708][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.712][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:55.713][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:55.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.715][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.719][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:55.720][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:55.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.721][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.730][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.731][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.733][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.737][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.738][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.740][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.744][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2025-06-28 16:01:55.745][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-06-28 16:01:55.746][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-06-28 16:01:55.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-28 16:01:55.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:55.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:55.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:55.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:55.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:55.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-06-28 16:01:55.757][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.758][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.760][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.764][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.765][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.766][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.767][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.770][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.771][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.773][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.774][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.777][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.778][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.779][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.780][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.783][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.784][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.786][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.787][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.790][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.791][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.792][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.794][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.797][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-06-28 16:01:55.798][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:55.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.799][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.800][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-06-28 16:01:55.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:55.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.804][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:55.804][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:55.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.806][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.807][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:55.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:55.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.810][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:55.811][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:55.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.813][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:55.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:55.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.817][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.818][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.819][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.824][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:55.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.828][ef$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:55.829][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:55.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.831][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.832][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:55.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:55.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.835][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-06-28 16:01:55.836][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:55.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.837][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-06-28 16:01:55.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:55.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.842][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.842][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.844][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.845][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:55.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.848][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.849][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.851][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.852][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:55.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.855][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-06-28 16:01:55.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.858][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.861][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:55.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.864][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-06-28 16:01:55.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.867][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.870][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:55.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.873][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-06-28 16:01:55.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.876][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.880][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:55.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.883][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-06-28 16:01:55.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.885][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.888][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:55.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.892][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-06-28 16:01:55.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.895][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.898][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:55.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:55.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:55.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.904][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.907][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.918][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-28 16:01:55.942][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2025-06-28 16:01:55.944][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:55.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:55.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.946][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:55.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:55.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.949][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:55.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:55.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.952][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-28 16:01:55.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-28 16:01:55.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.955][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-28 16:01:55.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-28 16:01:55.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.958][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-06-28 16:01:55.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-06-28 16:01:55.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.961][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-06-28 16:01:55.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-06-28 16:01:55.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.971][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:55.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:55.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:55.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:55.999][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:55.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:56.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.006][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:56.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:56.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.009][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:56.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:56.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:56.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:56.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:56.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:56.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:56.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:56.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.027][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:56.028][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:56.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.030][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:56.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:56.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:56.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:56.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:56.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:56.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:56.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:56.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.051][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:56.052][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:56.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.053][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:56.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:56.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.073][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.074][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.075][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.085][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:56.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:56.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.088][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:56.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:56.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.091][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:56.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:56.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.094][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:56.099][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:56.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.101][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.102][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:56.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:56.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.111][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:56.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:56.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.114][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:56.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:56.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.117][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:56.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:56.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.120][ef$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:56.121][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:56.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.122][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.123][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:56.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:56.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.132][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:56.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:56.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.135][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:56.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:56.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.138][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:56.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:56.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.141][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:56.142][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:56.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.143][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.144][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:56.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:56.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.154][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:56.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:56.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.157][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:56.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:56.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.160][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:56.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:56.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.164][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:56.164][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:56.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.166][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.167][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:56.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:56.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.177][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:56.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:56.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:56.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:56.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.184][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:56.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:56.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.192][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:56.193][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:56.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.195][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.196][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:56.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:56.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.206][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:56.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:56.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.209][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:56.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:56.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.212][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:56.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:56.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.215][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:56.216][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:56.217][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.218][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:56.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:56.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.228][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:56.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:56.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.232][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:56.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:56.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.235][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:56.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:56.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.238][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:56.238][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:56.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.240][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.240][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:56.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:56.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.251][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:56.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:56.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.254][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:56.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:56.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.257][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:56.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:56.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.260][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:56.261][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:56.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.263][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.264][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:56.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:56.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.274][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:56.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:56.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.278][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:56.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:56.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.281][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:56.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:56.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.289][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:56.290][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:56.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.292][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.293][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:56.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:56.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.303][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:56.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:56.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.306][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:56.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:56.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.309][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:56.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:56.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.313][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:56.313][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:56.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.315][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.316][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:56.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:56.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.326][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:56.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:56.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.330][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:56.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:56.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.333][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:56.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:56.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.336][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:56.337][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:56.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.339][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.340][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:56.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:56.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.350][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:56.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:56.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.353][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:56.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:56.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:56.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:56.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.359][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:56.360][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:56.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.361][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.362][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:56.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:56.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.373][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:56.373][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:56.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.375][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.380][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:56.385][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-06-28 16:01:56.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.387][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.392][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:56.393][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-06-28 16:01:56.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.394][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.399][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:56.400][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-06-28 16:01:56.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.401][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.406][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:56.407][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-06-28 16:01:56.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.408][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.413][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:56.414][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-06-28 16:01:56.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.415][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.420][ef$get] Asked field names are: formula.
biodb.TRACE[2025-06-28 16:01:56.420][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-06-28 16:01:56.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.422][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.426][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-06-28 16:01:56.427][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-06-28 16:01:56.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.428][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.433][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-06-28 16:01:56.433][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-06-28 16:01:56.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.435][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.439][ef$get] Asked field names are: logp.
biodb.TRACE[2025-06-28 16:01:56.440][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-06-28 16:01:56.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.441][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.446][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.447][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.448][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.452][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:56.453][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-06-28 16:01:56.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.455][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.459][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:56.460][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:56.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.462][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.466][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:56.467][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-06-28 16:01:56.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.468][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.473][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:56.474][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-06-28 16:01:56.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.475][ef$get] fields variable is a list.
biodb.INFO [2025-06-28 16:01:56.483][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.483][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-06-28 16:01:56.484][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:56.490][biodb::testThat]
biodb.DEBUG[2025-06-28 16:01:56.492][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-06-28 16:01:56.494][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-06-28 16:01:56.495][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
fscache.DEBUG[2025-06-28 16:01:56.501][FUN] Found encoding ISO-8859-1 for file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/65124.xml.
biodb.DEBUG[2025-06-28 16:01:56.502][conn$getEntryContent] 1 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:56.503][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:56.503][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:56.504][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:56.505][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-06-28 16:01:56.517][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.518][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-06-28 16:01:56.519][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:56.519][biodb::testThat]
biodb.TRACE[2025-06-28 16:01:56.522][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:56.523][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:56.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.524][ef$get] fields variable is a list.
biodb.DEBUG[2025-06-28 16:01:56.525][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2025-06-28 16:01:56.533][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-06-28 16:01:56.534][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-06-28 16:01:56.536][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-06-28 16:01:56.536][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:56.537][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:56.538][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:56.539][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:56.540][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-06-28 16:01:56.551][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.552][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-06-28 16:01:56.553][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:56.553][biodb::testThat]
biodb.DEBUG[2025-06-28 16:01:56.560][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-06-28 16:01:56.561][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-06-28 16:01:56.562][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-06-28 16:01:56.562][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:56.563][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:56.564][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:56.565][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:56.565][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-06-28 16:01:56.577][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.578][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-06-28 16:01:56.579][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:56.579][biodb::testThat]
biodb.DEBUG[2025-06-28 16:01:56.582][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-06-28 16:01:56.583][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-06-28 16:01:56.584][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-06-28 16:01:56.585][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:56.590][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:56.591][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:56.592][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:56.593][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-06-28 16:01:56.604][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.605][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-06-28 16:01:56.606][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:56.607][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.619][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.620][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-06-28 16:01:56.621][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:56.621][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.633][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.634][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-06-28 16:01:56.635][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:56.635][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.647][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.648][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-06-28 16:01:56.649][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:56.649][biodb::testThat]
biodb.TRACE[2025-06-28 16:01:56.667][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:56.668][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:56.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.670][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.670][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.671][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.677][ef$get] fields variable is a list.
biodb.INFO [2025-06-28 16:01:56.678][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.679][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-06-28 16:01:56.680][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:56.681][biodb::testThat]
biodb.DEBUG[2025-06-28 16:01:56.687][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-06-28 16:01:56.688][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-06-28 16:01:56.689][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-06-28 16:01:56.690][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:56.691][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:56.692][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:56.693][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:56.694][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-06-28 16:01:56.705][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.706][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-06-28 16:01:56.707][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:56.708][biodb::testThat]
biodb.DEBUG[2025-06-28 16:01:56.710][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-06-28 16:01:56.711][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-06-28 16:01:56.712][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
fscache.DEBUG[2025-06-28 16:01:56.716][FUN] Found encoding ISO-8859-1 for file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/65124.xml.
biodb.DEBUG[2025-06-28 16:01:56.717][conn$getEntryContent] 1 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:56.717][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:56.718][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:56.719][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:56.720][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-06-28 16:01:56.731][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.732][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-06-28 16:01:56.733][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:56.734][biodb::testThat]
biodb.DEBUG[2025-06-28 16:01:56.736][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-06-28 16:01:56.737][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-06-28 16:01:56.738][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
fscache.DEBUG[2025-06-28 16:01:56.741][FUN] Found encoding ISO-8859-1 for file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/65124.xml.
biodb.DEBUG[2025-06-28 16:01:56.742][conn$getEntryContent] 1 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:56.743][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:56.744][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:56.745][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:56.746][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-06-28 16:01:56.757][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.758][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-06-28 16:01:56.759][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:56.760][biodb::testThat]
biodb.DEBUG[2025-06-28 16:01:56.762][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-06-28 16:01:56.763][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-06-28 16:01:56.765][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
fscache.DEBUG[2025-06-28 16:01:56.768][FUN] Found encoding ISO-8859-1 for file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/65124.xml.
biodb.DEBUG[2025-06-28 16:01:56.769][conn$getEntryContent] 1 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:56.770][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:56.770][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:56.771][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:56.772][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.TRACE[2025-06-28 16:01:56.788][ef$get] Asked field names are: name.
biodb.TRACE[2025-06-28 16:01:56.789][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-06-28 16:01:56.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.791][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:56.792][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.793][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-06-28 16:01:56.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:56.794][ef$get] fields variable is a list.
biodb.INFO [2025-06-28 16:01:56.796][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.797][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-06-28 16:01:56.797][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:56.798][biodb::testThat]
biodb.DEBUG[2025-06-28 16:01:56.801][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-06-28 16:01:56.802][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-06-28 16:01:56.803][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
fscache.DEBUG[2025-06-28 16:01:56.806][FUN] Found encoding ISO-8859-1 for file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/65124.xml.
biodb.DEBUG[2025-06-28 16:01:56.807][conn$getEntryContent] 1 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:56.808][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:56.809][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:56.809][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:56.810][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-06-28 16:01:56.821][biodb::testThat]
biodb.INFO [2025-06-28 16:01:56.822][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-06-28 16:01:56.823][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:56.824][biodb::testThat]
biodb.DEBUG[2025-06-28 16:01:56.826][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-06-28 16:01:56.827][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-06-28 16:01:56.828][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
fscache.DEBUG[2025-06-28 16:01:56.832][FUN] Found encoding ISO-8859-1 for file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/65124.xml.
biodb.DEBUG[2025-06-28 16:01:56.833][conn$getEntryContent] 1 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:56.833][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:56.834][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-06-28 16:01:56.835][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-06-28 16:01:56.836][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-06-28 16:01:56.847][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-06-28 16:01:56.848][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2025-06-28 16:01:56.849][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-06-28 16:01:56.850][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:56.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:56.851][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:56.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:56.852][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-06-28 16:01:56.856][biodb::testContext]
biodb.INFO [2025-06-28 16:01:56.857][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-28 16:01:56.858][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2025-06-28 16:01:56.859][biodb::testContext] ********************************************************************************
biodb.INFO [2025-06-28 16:01:56.859][biodb::testContext]
biodb.INFO [2025-06-28 16:01:56.861][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-06-28 16:01:56.863][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-06-28 16:01:56.866][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-28 16:01:56.867][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-06-28 16:01:56.867][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-06-28 16:01:56.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:56.875][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-06-28 16:01:56.876][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-06-28 16:01:56.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:56.879][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-06-28 16:01:56.880][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-06-28 16:01:56.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:56.882][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-06-28 16:01:56.883][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-06-28 16:01:56.884][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-06-28 16:01:56.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:56.887][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-06-28 16:01:56.888][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-06-28 16:01:56.889][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-06-28 16:01:56.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:56.892][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-06-28 16:01:56.893][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-06-28 16:01:56.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:56.896][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-06-28 16:01:56.897][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-06-28 16:01:56.898][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-06-28 16:01:56.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:56.901][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-06-28 16:01:56.901][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-06-28 16:01:56.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:56.904][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-06-28 16:01:56.905][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-06-28 16:01:56.905][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-06-28 16:01:56.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:56.908][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-06-28 16:01:56.909][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-06-28 16:01:56.910][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-06-28 16:01:56.911][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-06-28 16:01:56.911][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-06-28 16:01:56.912][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-06-28 16:01:56.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:56.915][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-06-28 16:01:56.915][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-06-28 16:01:56.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.918][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[2025-06-28 16:01:56.918][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-06-28 16:01:56.919][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-06-28 16:01:56.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:56.922][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-06-28 16:01:56.923][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-06-28 16:01:56.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.925][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[2025-06-28 16:01:56.925][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-06-28 16:01:56.926][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-06-28 16:01:56.927][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-06-28 16:01:56.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:56.930][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-06-28 16:01:56.931][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-06-28 16:01:56.948][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-06-28 16:01:56.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.951][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[2025-06-28 16:01:56.952][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-06-28 16:01:56.953][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-06-28 16:01:56.954][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-06-28 16:01:56.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:56.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:56.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:56.957][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-06-28 16:01:56.958][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:56.959][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-06-28 16:01:56.959][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:56.960][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:56.961][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:56.962][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:56.963][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:56.964][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:56.964][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-28 16:01:56.965][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:56.966][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:56.967][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-06-28 16:01:56.968][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:56.969][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:56.969][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:56.970][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:56.970][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-28 16:01:56.970][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-28 16:01:56.970][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-28 16:01:56.970][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-28 16:01:56.971][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:56.972][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:56.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:56.973][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:56.978][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:56.979][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:56.980][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:56.981][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:56.982][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:56.982][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:56.983][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:56.984][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:56.985][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-06-28 16:01:56.986][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:56.987][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-06-28 16:01:56.988][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:56.988][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:56.989][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:56.990][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:56.991][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:56.992][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:56.992][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-28 16:01:56.993][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:56.994][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:56.995][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-06-28 16:01:56.996][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:56.996][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:56.997][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:56.998][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:56.998][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-28 16:01:56.998][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-28 16:01:56.998][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-06-28 16:01:56.998][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-06-28 16:01:56.999][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:57.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:57.000][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:57.001][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:57.002][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:57.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:57.003][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.004][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:57.005][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:57.005][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:57.006][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:57.007][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:57.008][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-06-28 16:01:57.009][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.010][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-06-28 16:01:57.010][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.011][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:57.012][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.013][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.014][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:57.014][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.015][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-06-28 16:01:57.016][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:57.017][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:57.017][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-06-28 16:01:57.018][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:57.019][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:57.019][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.020][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:57.021][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:57.022][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:57.023][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:57.023][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:57.024][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:57.025][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:57.025][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.026][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:57.027][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:57.028][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:57.028][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:57.029][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:57.030][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-06-28 16:01:57.031][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.032][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-06-28 16:01:57.033][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.034][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:57.035][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.035][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.036][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:57.037][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.038][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-06-28 16:01:57.038][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:57.039][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:57.040][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-06-28 16:01:57.041][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:57.042][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:57.042][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.043][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:57.044][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-06-28 16:01:57.045][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:57.045][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:57.046][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:57.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:57.048][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:57.048][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.049][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:57.050][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:57.051][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:57.051][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:57.052][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:57.053][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-28 16:01:57.054][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.102][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[2025-06-28 16:01:57.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.106][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[2025-06-28 16:01:57.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.113][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[2025-06-28 16:01:57.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.119][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[2025-06-28 16:01:57.120][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-06-28 16:01:57.121][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-06-28 16:01:57.122][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-06-28 16:01:57.123][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-06-28 16:01:57.124][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-06-28 16:01:57.125][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-06-28 16:01:57.126][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-06-28 16:01:57.127][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-06-28 16:01:57.128][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-06-28 16:01:57.129][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-06-28 16:01:57.130][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-06-28 16:01:57.131][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-06-28 16:01:57.132][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-06-28 16:01:57.133][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-06-28 16:01:57.134][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-06-28 16:01:57.135][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-06-28 16:01:57.137][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-06-28 16:01:57.138][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-06-28 16:01:57.139][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-06-28 16:01:57.140][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-06-28 16:01:57.141][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-06-28 16:01:57.142][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-06-28 16:01:57.143][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-06-28 16:01:57.144][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-06-28 16:01:57.145][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-06-28 16:01:57.147][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-06-28 16:01:57.152][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-06-28 16:01:57.154][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-06-28 16:01:57.155][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-06-28 16:01:57.156][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-06-28 16:01:57.157][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-06-28 16:01:57.158][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-06-28 16:01:57.159][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-06-28 16:01:57.160][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-06-28 16:01:57.162][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-06-28 16:01:57.163][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-06-28 16:01:57.164][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-06-28 16:01:57.165][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-06-28 16:01:57.166][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-06-28 16:01:57.167][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-06-28 16:01:57.168][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-06-28 16:01:57.169][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-06-28 16:01:57.170][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-06-28 16:01:57.171][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-06-28 16:01:57.173][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-06-28 16:01:57.174][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-06-28 16:01:57.175][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-06-28 16:01:57.176][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-06-28 16:01:57.177][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-06-28 16:01:57.178][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-06-28 16:01:57.179][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-06-28 16:01:57.180][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-06-28 16:01:57.181][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-06-28 16:01:57.182][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-06-28 16:01:57.183][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-06-28 16:01:57.184][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-06-28 16:01:57.185][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-06-28 16:01:57.186][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-06-28 16:01:57.187][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-06-28 16:01:57.188][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-06-28 16:01:57.189][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-06-28 16:01:57.190][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-06-28 16:01:57.191][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-06-28 16:01:57.192][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-06-28 16:01:57.193][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-06-28 16:01:57.195][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-06-28 16:01:57.196][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-06-28 16:01:57.197][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-06-28 16:01:57.198][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-06-28 16:01:57.199][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-06-28 16:01:57.200][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-06-28 16:01:57.201][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-06-28 16:01:57.202][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-06-28 16:01:57.203][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-06-28 16:01:57.204][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-06-28 16:01:57.205][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-06-28 16:01:57.206][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-06-28 16:01:57.207][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-06-28 16:01:57.208][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-06-28 16:01:57.210][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-06-28 16:01:57.211][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-06-28 16:01:57.212][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-06-28 16:01:57.213][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-06-28 16:01:57.214][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-06-28 16:01:57.216][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-06-28 16:01:57.216][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-06-28 16:01:57.217][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.219][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.244][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[2025-06-28 16:01:57.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-06-28 16:01:57.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-06-28 16:01:57.306][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-06-28 16:01:57.307][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-06-28 16:01:57.309][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.309][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-06-28 16:01:57.310][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.311][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:57.312][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.313][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.313][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.314][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.315][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-06-28 16:01:57.316][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:57.317][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.317][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-06-28 16:01:57.318][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:57.323][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-06-28 16:01:57.323][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-06-28 16:01:57.324][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:57.325][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:57.326][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-06-28 16:01:57.327][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:57.328][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:57.329][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:57.329][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:57.330][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:57.331][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.332][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-06-28 16:01:57.332][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-06-28 16:01:57.333][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:57.333][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:57.334][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.335][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:57.336][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-06-28 16:01:57.337][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.338][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-06-28 16:01:57.339][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.340][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:57.341][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.341][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.342][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.343][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.344][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-28 16:01:57.345][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:57.345][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.346][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-06-28 16:01:57.347][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:57.348][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-06-28 16:01:57.348][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-06-28 16:01:57.348][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-06-28 16:01:57.348][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-06-28 16:01:57.348][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-06-28 16:01:57.348][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-06-28 16:01:57.349][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:57.349][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:57.350][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-06-28 16:01:57.351][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:57.352][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:57.353][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:57.353][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:57.354][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:57.355][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.356][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:57.356][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-06-28 16:01:57.356][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:57.357][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:57.358][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.359][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:57.360][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-06-28 16:01:57.361][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:57.362][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-06-28 16:01:57.363][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.363][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:57.364][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.365][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.366][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.367][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.367][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-28 16:01:57.368][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:57.369][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.370][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-06-28 16:01:57.371][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:57.371][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-06-28 16:01:57.371][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:57.371][self$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[2025-06-28 16:01:57.371][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:57.371][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:57.371][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:57.371][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:57.371][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:57.371][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:57.371][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:57.371][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-06-28 16:01:57.371][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:57.371][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:57.371][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-06-28 16:01:57.372][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:57.373][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-06-28 16:01:57.373][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-06-28 16:01:57.373][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-06-28 16:01:57.374][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-06-28 16:01:57.375][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:57.375][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:57.376][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:57.377][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:57.378][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:57.378][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.379][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:57.379][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-06-28 16:01:57.379][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-06-28 16:01:57.380][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:57.381][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:57.382][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.382][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-06-28 16:01:57.383][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-06-28 16:01:57.385][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.386][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-06-28 16:01:57.386][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.387][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-06-28 16:01:57.388][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.389][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.389][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.390][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.391][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-06-28 16:01:57.392][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-06-28 16:01:57.393][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.393][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-06-28 16:01:57.394][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-06-28 16:01:57.395][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-06-28 16:01:57.395][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-06-28 16:01:57.396][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-06-28 16:01:57.397][self$setPropertyValue]
biodb.DEBUG[2025-06-28 16:01:57.397][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-06-28 16:01:57.398][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:57.399][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:57.400][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-06-28 16:01:57.400][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-06-28 16:01:57.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-06-28 16:01:57.402][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-06-28 16:01:57.403][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-06-28 16:01:57.403][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-06-28 16:01:57.403][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-06-28 16:01:57.404][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-06-28 16:01:57.404][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-06-28 16:01:57.405][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-06-28 16:01:57.410][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-06-28 16:01:57.411][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-06-28 16:01:57.413][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-06-28 16:01:57.414][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-06-28 16:01:57.415][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-06-28 16:01:57.417][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-06-28 16:01:57.418][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-06-28 16:01:57.422][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2025-06-28 16:01:57.429][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2025-06-28 16:01:57.433][biodb::testThat]
biodb.INFO [2025-06-28 16:01:57.433][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-06-28 16:01:57.434][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:57.435][biodb::testThat]
biodb.TRACE[2025-06-28 16:01:57.437][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2025-06-28 16:01:57.438][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-06-28 16:01:57.441][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-06-28 16:01:57.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-28 16:01:57.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.450][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-06-28 16:01:57.453][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.454][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.455][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.460][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.461][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.462][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.463][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.467][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.470][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.476][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-28 16:01:57.499][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2025-06-28 16:01:57.505][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:57.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:57.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.509][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:57.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:57.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.512][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:57.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:57.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.515][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-28 16:01:57.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-28 16:01:57.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.519][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-28 16:01:57.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-28 16:01:57.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.522][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-06-28 16:01:57.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-06-28 16:01:57.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.525][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-06-28 16:01:57.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-06-28 16:01:57.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.536][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.563][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.566][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.569][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.587][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.588][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.594][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.605][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.608][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.612][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.615][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.615][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.617][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.618][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.628][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.629][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.631][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.635][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.636][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.638][ef$get] fields variable is a list.
biodb.INFO [2025-06-28 16:01:57.645][biodb::testThat]
biodb.INFO [2025-06-28 16:01:57.646][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-06-28 16:01:57.647][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:57.647][biodb::testThat]
biodb.DEBUG[2025-06-28 16:01:57.649][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-06-28 16:01:57.651][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-06-28 16:01:57.652][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
fscache.DEBUG[2025-06-28 16:01:57.656][FUN] Found encoding ISO-8859-1 for file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75/3.xml.
biodb.DEBUG[2025-06-28 16:01:57.657][conn$getEntryContent] 1 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-06-28 16:01:57.658][self$createEntryFromContent] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-06-28 16:01:57.659][self$createEntryFromContent] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-06-28 16:01:57.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-06-28 16:01:57.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-06-28 16:01:57.670][ef$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.671][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.673][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.677][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.678][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.679][ef$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.680][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-06-28 16:01:57.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.683][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.692][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.698][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-06-28 16:01:57.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-06-28 16:01:57.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-06-28 16:01:57.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-06-28 16:01:57.721][self$createEntryFromContent] Accession numbers: 3.
biodb.TRACE[2025-06-28 16:01:57.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-06-28 16:01:57.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-06-28 16:01:57.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-06-28 16:01:57.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-06-28 16:01:57.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-06-28 16:01:57.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-06-28 16:01:57.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-06-28 16:01:57.739][biodb::testThat]
biodb.INFO [2025-06-28 16:01:57.740][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-06-28 16:01:57.740][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:57.741][biodb::testThat]
biodb.INFO [2025-06-28 16:01:57.747][biodb::testThat]
biodb.INFO [2025-06-28 16:01:57.748][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-06-28 16:01:57.748][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:57.749][biodb::testThat]
biodb.WARN [2025-06-28 16:01:57.752][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-06-28 16:01:57.755][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-06-28 16:01:57.763][biodb::testThat]
biodb.INFO [2025-06-28 16:01:57.764][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-06-28 16:01:57.765][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:57.765][biodb::testThat]
biodb.TRACE[2025-06-28 16:01:57.775][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:57.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:57.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.778][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:57.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:57.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.787][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:57.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:57.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.790][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-28 16:01:57.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-28 16:01:57.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.793][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-28 16:01:57.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-28 16:01:57.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.797][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-06-28 16:01:57.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-06-28 16:01:57.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.800][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-06-28 16:01:57.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-06-28 16:01:57.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.811][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:57.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:57.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.814][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-06-28 16:01:57.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-06-28 16:01:57.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.818][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:57.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-06-28 16:01:57.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.821][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-28 16:01:57.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-28 16:01:57.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.824][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-06-28 16:01:57.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-06-28 16:01:57.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.827][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-06-28 16:01:57.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-06-28 16:01:57.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-06-28 16:01:57.831][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-06-28 16:01:57.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-06-28 16:01:57.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-06-28 16:01:57.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-06-28 16:01:57.839][biodb::testThat]
biodb.INFO [2025-06-28 16:01:57.840][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-06-28 16:01:57.841][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:57.842][biodb::testThat]
biodb.INFO [2025-06-28 16:01:57.855][biodb::testThat]
biodb.INFO [2025-06-28 16:01:57.856][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-06-28 16:01:57.858][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:57.859][biodb::testThat]
biodb.INFO [2025-06-28 16:01:57.877][biodb::testThat]
biodb.INFO [2025-06-28 16:01:57.878][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-06-28 16:01:57.879][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:57.880][biodb::testThat]
biodb.INFO [2025-06-28 16:01:57.891][biodb::testThat]
biodb.INFO [2025-06-28 16:01:57.892][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-06-28 16:01:57.893][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-06-28 16:01:57.893][biodb::testThat]
biodb.INFO [2025-06-28 16:01:57.905][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-06-28 16:01:57.906][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2025-06-28 16:01:57.907][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-06-28 16:01:57.907][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-06-28 16:01:57.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-06-28 16:01:57.909][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-06-28 16:01:57.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-06-28 16:01:57.910][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-06-28 16:01:57.911][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 29 | WARN 1 | SKIP 0 | PASS 252 ]

══ 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$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$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 29 | WARN 1 | SKIP 0 | PASS 252 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNcbi/DESCRIPTION’ ... OK
* this is package ‘biodbNcbi’ version ‘1.13.0’
* 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 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:
   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 29 | WARN 1 | SKIP 0 | PASS 252 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbNcbi.Rcheck/00install.out

* installing *source* package ‘biodbNcbi’ ...
** this is package ‘biodbNcbi’ version ‘1.13.0’
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNcbi)