Back to Long Tests report for BioC 3.21

This page was generated on 2025-04-26 23:55 -0400 (Sat, 26 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4832
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4574
merida1macOS 12.7.5 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
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 8/30HostnameOS / ArchCHECK
biodbNcbi 1.12.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-04-26 09:55 -0400 (Sat, 26 Apr 2025)
git_url: https://git.bioconductor.org/packages/biodbNcbi
git_branch: RELEASE_3_21
git_last_commit: eff8ab9
git_last_commit_date: 2025-04-15 12:47:49 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  WARNINGS  

CHECK results for biodbNcbi on palomino7

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: 1.12.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.12.0.tar.gz
StartedAt: 2025-04-26 16:03:28 -0400 (Sat, 26 Apr 2025)
EndedAt: 2025-04-26 16:04:52 -0400 (Sat, 26 Apr 2025)
EllapsedTime: 83.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNcbi.Rcheck
Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


R version 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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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 [2025-04-26 16:04:23.775][biodb::testContext]
biodb.INFO [2025-04-26 16:04:23.778][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:04:23.779][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2025-04-26 16:04:23.781][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:04:23.782][biodb::testContext]
biodb.INFO [2025-04-26 16:04:23.788][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-26 16:04:23.791][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-26 16:04:23.799][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:04:23.800][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-26 16:04:23.801][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-26 16:04:23.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:23.806][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-26 16:04:23.822][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-26 16:04:23.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.825][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[2025-04-26 16:04:23.826][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-26 16:04:23.827][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-26 16:04:23.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:23.832][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-26 16:04:23.833][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-26 16:04:23.834][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-26 16:04:23.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.837][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[2025-04-26 16:04:23.838][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-26 16:04:23.840][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-26 16:04:23.841][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-26 16:04:23.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:23.845][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-26 16:04:23.846][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-26 16:04:23.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:23.851][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-26 16:04:23.852][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-26 16:04:23.853][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-26 16:04:23.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:23.857][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-26 16:04:23.859][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-26 16:04:23.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:23.863][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-26 16:04:23.864][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-26 16:04:23.865][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-26 16:04:23.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:23.870][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:04:23.871][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-26 16:04:23.872][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-26 16:04:23.873][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-26 16:04:23.875][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-26 16:04:23.876][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-26 16:04:23.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:23.880][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-26 16:04:23.881][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-26 16:04:23.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:23.886][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-26 16:04:23.887][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-26 16:04:23.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:23.891][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-26 16:04:23.893][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-26 16:04:23.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:23.897][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-26 16:04:23.898][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-26 16:04:23.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:23.902][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-26 16:04:23.904][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-26 16:04:23.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:23.908][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:04:23.909][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-26 16:04:23.912][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-26 16:04:23.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:23.917][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-26 16:04:23.918][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-26 16:04:23.919][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-26 16:04:23.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:23.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:23.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:23.926][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-26 16:04:23.953][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:23.974][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-26 16:04:23.976][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:23.977][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:23.978][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:23.979][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:23.980][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:23.981][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:23.983][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:04:23.984][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:23.985][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:23.986][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-26 16:04:23.987][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:23.989][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:23.990][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:23.991][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:23.991][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:04:23.991][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:04:23.991][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:04:23.991][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:04:23.992][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:23.994][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:23.995][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:23.996][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:23.997][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:23.998][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:23.999][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.000][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.001][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:24.002][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:24.004][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:24.005][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.006][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-26 16:04:24.008][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:24.009][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:04:24.011][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.012][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:24.013][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.014][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.015][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:24.016][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.018][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:04:24.019][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:24.020][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.021][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-26 16:04:24.022][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:24.024][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.025][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.026][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:24.026][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:04:24.026][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:04:24.026][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:04:24.026][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:04:24.027][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:24.028][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:24.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:24.031][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:24.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:24.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:24.034][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.035][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.036][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:24.037][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:24.038][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:24.040][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.041][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-26 16:04:24.043][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.044][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-26 16:04:24.045][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.046][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:24.048][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.049][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.050][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:24.051][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.052][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:04:24.054][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:24.055][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:24.056][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-26 16:04:24.057][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:24.058][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.059][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.061][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.062][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:24.063][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:24.064][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:24.065][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:24.066][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:24.067][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:24.069][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.070][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.071][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:24.072][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:24.073][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:24.075][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.077][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-26 16:04:24.080][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.082][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:04:24.084][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.085][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:24.086][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.088][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.089][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:24.090][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.091][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:04:24.092][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:24.094][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:24.095][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-26 16:04:24.096][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:24.097][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.098][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.099][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.101][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:24.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:24.103][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:24.104][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:24.105][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:24.106][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:24.107][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.109][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.110][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:24.111][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:24.112][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:24.113][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.117][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:04:24.118][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.119][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[2025-04-26 16:04:24.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.178][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[2025-04-26 16:04:24.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.216][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-26 16:04:24.220][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-26 16:04:24.221][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-26 16:04:24.223][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-26 16:04:24.224][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-26 16:04:24.226][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-26 16:04:24.228][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-26 16:04:24.229][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-26 16:04:24.231][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-26 16:04:24.232][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-26 16:04:24.234][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-26 16:04:24.235][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-26 16:04:24.237][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-26 16:04:24.238][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-26 16:04:24.240][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-26 16:04:24.241][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-26 16:04:24.243][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-26 16:04:24.244][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-26 16:04:24.246][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-26 16:04:24.248][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-26 16:04:24.249][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-26 16:04:24.251][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-26 16:04:24.252][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-26 16:04:24.254][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-26 16:04:24.255][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-26 16:04:24.257][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-26 16:04:24.258][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-26 16:04:24.260][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-26 16:04:24.261][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-26 16:04:24.263][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-26 16:04:24.265][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-26 16:04:24.266][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-26 16:04:24.268][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-26 16:04:24.269][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-26 16:04:24.271][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-26 16:04:24.272][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-26 16:04:24.274][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-26 16:04:24.275][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-26 16:04:24.277][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-26 16:04:24.278][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-26 16:04:24.280][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-26 16:04:24.282][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-26 16:04:24.283][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-26 16:04:24.285][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-26 16:04:24.286][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-26 16:04:24.288][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-26 16:04:24.289][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-26 16:04:24.291][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-26 16:04:24.292][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-26 16:04:24.294][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-26 16:04:24.296][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-26 16:04:24.297][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-26 16:04:24.299][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-26 16:04:24.300][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-26 16:04:24.302][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-26 16:04:24.303][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-26 16:04:24.305][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-26 16:04:24.306][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-26 16:04:24.308][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-26 16:04:24.310][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-26 16:04:24.311][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-26 16:04:24.313][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-26 16:04:24.314][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-26 16:04:24.316][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-26 16:04:24.317][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-26 16:04:24.319][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-26 16:04:24.320][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-26 16:04:24.322][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-26 16:04:24.323][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-26 16:04:24.325][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-26 16:04:24.326][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-26 16:04:24.328][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-26 16:04:24.330][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-26 16:04:24.331][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-26 16:04:24.333][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-26 16:04:24.334][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-26 16:04:24.336][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-26 16:04:24.337][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-26 16:04:24.339][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-26 16:04:24.340][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-26 16:04:24.342][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-26 16:04:24.343][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-26 16:04:24.345][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-26 16:04:24.369][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-26 16:04:24.371][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-26 16:04:24.374][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:04:24.375][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.378][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.390][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[2025-04-26 16:04:24.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:24.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:24.542][bdb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-04-26 16:04:24.551][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-04-26 16:04:24.553][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.554][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-04-26 16:04:24.556][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.557][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:24.558][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.559][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.560][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.562][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.563][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-04-26 16:04:24.564][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:24.565][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.566][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-04-26 16:04:24.567][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:24.569][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-04-26 16:04:24.569][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-04-26 16:04:24.570][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:24.571][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.572][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-26 16:04:24.573][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:24.574][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:24.575][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:24.577][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:24.578][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:24.579][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.580][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-04-26 16:04:24.580][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-04-26 16:04:24.581][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:24.582][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:24.583][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.585][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.586][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-04-26 16:04:24.588][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.589][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-04-26 16:04:24.590][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.591][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:24.593][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.594][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.595][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.596][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.597][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-26 16:04:24.598][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:24.600][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.601][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-04-26 16:04:24.602][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:24.603][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-04-26 16:04:24.603][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-04-26 16:04:24.603][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-04-26 16:04:24.603][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-04-26 16:04:24.603][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-04-26 16:04:24.603][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-04-26 16:04:24.604][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:24.606][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:24.607][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-26 16:04:24.608][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:24.609][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:24.610][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:24.611][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:24.612][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:24.613][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.615][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-04-26 16:04:24.615][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-04-26 16:04:24.616][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:24.617][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:24.618][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.619][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.620][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-04-26 16:04:24.623][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:24.624][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-04-26 16:04:24.625][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.626][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:24.627][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.628][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.629][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.631][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.632][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-26 16:04:24.633][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:24.634][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.635][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-04-26 16:04:24.637][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:24.638][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-04-26 16:04:24.638][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:24.638][self$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[2025-04-26 16:04:24.638][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:24.638][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:24.638][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:24.638][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:24.638][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:24.638][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:24.638][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:24.638][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-04-26 16:04:24.638][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:24.638][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:24.638][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:24.644][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:24.645][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:24.645][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:04:24.645][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:04:24.646][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-04-26 16:04:24.647][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:24.648][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:24.649][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:24.650][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:24.652][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:24.653][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.654][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-04-26 16:04:24.654][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-04-26 16:04:24.654][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-04-26 16:04:24.655][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:24.656][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:24.657][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.658][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-04-26 16:04:24.660][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-04-26 16:04:24.662][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.663][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-04-26 16:04:24.664][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.665][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:24.666][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.667][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.669][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.671][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.673][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-26 16:04:24.675][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:24.676][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.678][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-04-26 16:04:24.680][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:24.681][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-04-26 16:04:24.681][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-04-26 16:04:24.682][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:24.683][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:24.689][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-04-26 16:04:24.691][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:24.692][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:24.693][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:24.694][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:24.695][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:24.696][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:24.698][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-04-26 16:04:24.698][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-04-26 16:04:24.698][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-04-26 16:04:24.699][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:24.700][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:24.701][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:24.702][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-04-26 16:04:24.708][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-04-26 16:04:24.710][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-26 16:04:24.711][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-26 16:04:24.713][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-04-26 16:04:24.714][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-26 16:04:24.716][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-04-26 16:04:24.737][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-04-26 16:04:24.738][initialize] Register connector ncbi.ccds with the request scheduler
biodb.DEBUG[2025-04-26 16:04:24.742][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.ccds.
biodb.DEBUG[2025-04-26 16:04:24.745][private$addConnectorRules] Create new rule for URL "www.ncbi.nlm.nih.gov" of connector "ncbi.ccds".
biodb.DEBUG[2025-04-26 16:04:24.749][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:04:24.750][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:04:24.752][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.ccds".
biodb.DEBUG[2025-04-26 16:04:24.753][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:04:24.755][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:04:24.756][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2025-04-26 16:04:24.766][biodb::testThat]
biodb.INFO [2025-04-26 16:04:24.767][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-04-26 16:04:24.769][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:24.770][biodb::testThat]
biodb.TRACE[2025-04-26 16:04:24.776][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2025-04-26 16:04:24.778][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:24.781][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-04-26 16:04:24.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:24.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:24.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:24.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:24.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:24.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:24.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:24.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:24.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:24.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:24.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:24.842][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:24.853][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:24.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:24.856][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:24.889][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:24.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:24.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:24.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:24.894][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:24.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:24.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:24.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:24.899][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:24.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:24.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:24.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:24.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:24.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:24.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:24.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:24.908][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:24.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:24.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:24.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:24.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:24.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:24.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:24.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:24.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:24.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:24.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:24.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:24.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:24.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:24.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:24.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:24.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:24.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:24.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:24.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:24.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:24.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:24.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:24.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:24.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:24.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:24.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:24.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:24.970][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2025-04-26 16:04:24.973][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:24.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:24.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:24.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:24.978][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:24.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:24.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:24.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.007][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:25.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:25.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.012][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:25.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:25.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.017][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:25.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:25.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.022][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:25.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:25.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.077][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.118][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.123][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.128][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.157][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.158][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.161][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.177][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:25.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.182][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.187][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.192][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:25.193][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.195][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.196][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:25.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.216][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.218][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.220][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.227][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.228][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.230][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.249][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2025-04-26 16:04:25.280][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:25.282][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-04-26 16:04:25.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:25.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:25.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:25.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:25.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:25.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:25.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:25.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.326][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:25.328][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.330][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.332][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:25.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.337][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.347][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.356][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:25.389][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2025-04-26 16:04:25.408][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.413][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.417][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:25.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:25.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.422][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:25.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:25.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.427][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:25.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:25.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.432][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:25.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:25.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.460][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.501][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.506][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.511][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.552][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.553][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.555][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.571][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:25.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.576][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.580][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.585][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:25.586][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.589][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.590][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:25.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.604][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.606][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.608][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.615][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.616][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.619][ef$get] fields variable is a list.
biodb.INFO [2025-04-26 16:04:25.631][biodb::testThat]
biodb.INFO [2025-04-26 16:04:25.632][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-26 16:04:25.633][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:25.634][biodb::testThat]
biodb.DEBUG[2025-04-26 16:04:25.637][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2025-04-26 16:04:25.643][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
biodb.TRACE[2025-04-26 16:04:25.650][cch$loadFileContent] Trying to load 2 files from cache: [2]: "CCDS12227.1, CCDS43240.1".
biodb.TRACE[2025-04-26 16:04:25.652][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-04-26 16:04:25.736][loadFileContents] Loaded 2 files from cache: [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS12227.1.html, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS43240.1.html".
biodb.DEBUG[2025-04-26 16:04:25.738][conn$getEntryContent] 2 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-04-26 16:04:25.740][self$createEntryFromContent] Creating NCBI CCDS entries from 2 content(s).
biodb.DEBUG[2025-04-26 16:04:25.741][self$createEntryFromContent] Parsing 2 NCBI CCDS entries.
biodb.DEBUG[2025-04-26 16:04:25.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:25.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:25.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:25.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:25.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:25.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:25.756][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:04:25.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.779][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:25.780][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.782][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.784][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:25.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.795][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.800][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.809][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:25.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:25.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:25.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:25.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:25.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:25.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:25.841][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.TRACE[2025-04-26 16:04:25.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.856][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:25.858][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.860][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.862][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:25.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:25.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.866][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.871][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.881][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:25.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:25.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:25.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:25.929][self$createEntryFromContent] Accession numbers: CCDS12227.1, CCDS43240.1.
biodb.TRACE[2025-04-26 16:04:25.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:25.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:25.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:25.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:25.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:25.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:25.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:25.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:25.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:25.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:25.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:25.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:25.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:25.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:25.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-26 16:04:25.982][biodb::testThat]
biodb.INFO [2025-04-26 16:04:25.983][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-26 16:04:25.984][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:25.985][biodb::testThat]
biodb.INFO [2025-04-26 16:04:25.994][biodb::testThat]
biodb.INFO [2025-04-26 16:04:25.995][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-04-26 16:04:25.997][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:25.998][biodb::testThat]
biodb.WARN [2025-04-26 16:04:26.016][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-04-26 16:04:26.033][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-04-26 16:04:26.046][biodb::testThat]
biodb.INFO [2025-04-26 16:04:26.047][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-04-26 16:04:26.048][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:26.049][biodb::testThat]
biodb.TRACE[2025-04-26 16:04:26.075][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:26.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:26.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:26.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:26.080][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:26.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:26.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:26.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:26.085][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:26.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:26.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:26.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:26.090][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:26.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:26.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:26.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:26.098][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:26.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:26.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:26.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:26.103][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:26.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:26.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:26.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:26.121][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:26.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:26.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:26.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:26.127][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:26.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:26.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:26.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:26.131][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:26.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:26.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:26.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:26.136][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:26.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:26.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:26.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:26.141][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:26.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:26.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:26.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:26.146][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:26.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:26.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:26.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-26 16:04:26.160][biodb::testThat]
biodb.INFO [2025-04-26 16:04:26.161][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-26 16:04:26.163][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:26.164][biodb::testThat]
biodb.INFO [2025-04-26 16:04:26.176][biodb::testThat]
biodb.INFO [2025-04-26 16:04:26.177][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-26 16:04:26.179][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:26.180][biodb::testThat]
biodb.INFO [2025-04-26 16:04:26.190][biodb::testThat]
biodb.INFO [2025-04-26 16:04:26.191][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-26 16:04:26.192][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:26.194][biodb::testThat]
biodb.DEBUG[2025-04-26 16:04:26.198][function(conn, opt)] Trying to download "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.DEBUG[2025-04-26 16:04:27.488][getUrlContent] Use RCurl for downloading content of URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1.
biodb.INFO [2025-04-26 16:04:28.632][biodb::testThat]
biodb.INFO [2025-04-26 16:04:28.633][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-26 16:04:28.635][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:28.636][biodb::testThat]
biodb.INFO [2025-04-26 16:04:28.645][bdb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-26 16:04:28.646][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.ccds from the request scheduler
biodb.INFO [2025-04-26 16:04:28.648][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-04-26 16:04:28.649][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-26 16:04:28.650][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:28.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:28.652][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:28.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:28.654][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-26 16:04:28.666][biodb::testContext]
biodb.INFO [2025-04-26 16:04:28.667][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:04:28.669][biodb::testContext] Test context - Gene long tests
biodb.INFO [2025-04-26 16:04:28.670][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:04:28.672][biodb::testContext]
biodb.INFO [2025-04-26 16:04:28.675][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-26 16:04:28.677][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-26 16:04:28.682][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:04:28.684][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-26 16:04:28.685][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-26 16:04:28.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.689][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-26 16:04:28.691][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-26 16:04:28.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.695][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-26 16:04:28.696][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-26 16:04:28.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.700][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-26 16:04:28.702][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-26 16:04:28.703][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-26 16:04:28.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.707][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-26 16:04:28.709][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-26 16:04:28.710][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-26 16:04:28.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.714][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-26 16:04:28.715][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-26 16:04:28.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.726][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-26 16:04:28.728][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-26 16:04:28.729][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-26 16:04:28.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.733][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-26 16:04:28.734][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-26 16:04:28.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.739][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-26 16:04:28.740][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-26 16:04:28.741][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-26 16:04:28.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.745][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:04:28.747][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-26 16:04:28.748][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-26 16:04:28.749][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-26 16:04:28.750][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-26 16:04:28.751][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-26 16:04:28.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.756][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-26 16:04:28.757][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-26 16:04:28.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.760][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[2025-04-26 16:04:28.761][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-26 16:04:28.763][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-26 16:04:28.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.767][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-26 16:04:28.768][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-26 16:04:28.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.773][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-26 16:04:28.774][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-26 16:04:28.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.778][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-26 16:04:28.780][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-26 16:04:28.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.784][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:04:28.785][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-26 16:04:28.788][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-26 16:04:28.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.793][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-26 16:04:28.794][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-26 16:04:28.795][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-26 16:04:28.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.800][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-26 16:04:28.802][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:28.803][self$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[2025-04-26 16:04:28.804][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.805][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:28.807][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.808][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:28.809][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:28.810][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:28.812][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:04:28.813][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:28.814][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.815][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-26 16:04:28.816][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:28.818][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:28.819][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.820][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:28.820][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:04:28.820][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:04:28.820][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:04:28.820][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:04:28.821][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:28.822][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:28.824][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:28.825][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:28.826][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:28.827][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:28.828][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:28.829][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:28.831][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:28.832][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:28.833][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:28.834][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:28.835][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-26 16:04:28.837][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:28.839][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:04:28.840][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.841][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:28.842][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.843][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:28.845][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:28.846][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:28.847][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:04:28.848][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:28.850][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.851][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-26 16:04:28.852][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:28.858][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:28.861][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.862][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:28.862][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:04:28.862][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:04:28.862][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:04:28.862][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:04:28.864][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:28.865][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:28.866][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:28.867][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:28.868][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:28.870][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:28.871][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:28.872][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:28.873][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:28.874][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:28.875][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:28.877][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:28.878][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-26 16:04:28.880][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.881][self$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[2025-04-26 16:04:28.882][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.883][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:28.885][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.886][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:28.887][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:28.888][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:28.889][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:04:28.891][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:28.892][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:28.893][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-26 16:04:28.894][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:28.896][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:28.897][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.898][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:28.899][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:28.900][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:28.902][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:28.903][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:28.904][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:28.905][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:28.906][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:28.907][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:28.908][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:28.910][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:28.911][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:28.912][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:28.913][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-26 16:04:28.915][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.916][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:04:28.918][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.919][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:28.920][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.921][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:28.922][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:28.924][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:28.925][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:04:28.926][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:28.927][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:28.929][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-26 16:04:28.930][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:28.931][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:28.932][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:28.933][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:28.935][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:28.936][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:28.937][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:28.938][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:28.939][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:28.940][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:28.942][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:28.943][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:28.944][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:28.945][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:28.946][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:28.947][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:28.949][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:04:28.950][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.951][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[2025-04-26 16:04:28.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:28.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:28.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:28.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:28.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:28.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:28.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:28.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:28.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:28.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:28.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:28.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:28.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:28.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:28.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:28.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:28.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:28.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:28.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:28.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.027][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[2025-04-26 16:04:29.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.033][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[2025-04-26 16:04:29.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.051][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-26 16:04:29.052][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-26 16:04:29.054][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-26 16:04:29.055][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-26 16:04:29.057][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-26 16:04:29.059][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-26 16:04:29.060][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-26 16:04:29.062][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-26 16:04:29.064][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-26 16:04:29.065][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-26 16:04:29.067][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-26 16:04:29.068][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-26 16:04:29.070][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-26 16:04:29.072][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-26 16:04:29.073][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-26 16:04:29.075][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-26 16:04:29.076][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-26 16:04:29.078][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-26 16:04:29.079][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-26 16:04:29.081][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-26 16:04:29.083][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-26 16:04:29.084][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-26 16:04:29.086][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-26 16:04:29.087][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-26 16:04:29.089][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-26 16:04:29.091][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-26 16:04:29.092][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-26 16:04:29.094][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-26 16:04:29.095][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-26 16:04:29.097][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-26 16:04:29.098][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-26 16:04:29.100][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-26 16:04:29.101][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-26 16:04:29.103][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-26 16:04:29.105][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-26 16:04:29.106][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-26 16:04:29.108][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-26 16:04:29.109][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-26 16:04:29.111][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-26 16:04:29.112][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-26 16:04:29.114][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-26 16:04:29.115][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-26 16:04:29.122][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-26 16:04:29.124][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-26 16:04:29.126][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-26 16:04:29.127][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-26 16:04:29.129][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-26 16:04:29.130][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-26 16:04:29.132][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-26 16:04:29.133][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-26 16:04:29.135][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-26 16:04:29.136][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-26 16:04:29.138][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-26 16:04:29.139][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-26 16:04:29.141][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-26 16:04:29.142][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-26 16:04:29.144][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-26 16:04:29.146][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-26 16:04:29.147][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-26 16:04:29.149][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-26 16:04:29.150][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-26 16:04:29.152][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-26 16:04:29.154][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-26 16:04:29.155][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-26 16:04:29.157][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-26 16:04:29.158][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-26 16:04:29.160][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-26 16:04:29.162][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-26 16:04:29.163][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-26 16:04:29.165][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-26 16:04:29.166][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-26 16:04:29.168][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-26 16:04:29.169][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-26 16:04:29.171][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-26 16:04:29.173][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-26 16:04:29.174][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-26 16:04:29.176][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-26 16:04:29.177][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-26 16:04:29.179][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-26 16:04:29.180][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-26 16:04:29.182][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-26 16:04:29.184][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-26 16:04:29.185][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-26 16:04:29.187][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-26 16:04:29.189][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-26 16:04:29.191][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:04:29.192][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.194][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.210][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[2025-04-26 16:04:29.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.225][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[2025-04-26 16:04:29.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.232][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[2025-04-26 16:04:29.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:29.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:29.331][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-04-26 16:04:29.334][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-04-26 16:04:29.336][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.337][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-04-26 16:04:29.338][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.339][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:29.341][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.342][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:29.343][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.344][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:29.345][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-04-26 16:04:29.347][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:29.348][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.349][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-04-26 16:04:29.350][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:29.351][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-04-26 16:04:29.351][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-04-26 16:04:29.353][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:29.354][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:29.355][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-26 16:04:29.356][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:29.357][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:29.358][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:29.359][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:29.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:29.362][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:29.363][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-04-26 16:04:29.363][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-04-26 16:04:29.364][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:29.365][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:29.366][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.367][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:29.369][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-04-26 16:04:29.371][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.372][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-04-26 16:04:29.373][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.379][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:29.381][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.382][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:29.383][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.384][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:29.385][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-26 16:04:29.386][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:29.388][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.389][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-04-26 16:04:29.390][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:29.391][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-04-26 16:04:29.391][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-04-26 16:04:29.391][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-04-26 16:04:29.391][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-04-26 16:04:29.391][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-04-26 16:04:29.391][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-04-26 16:04:29.392][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:29.393][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:29.395][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-26 16:04:29.396][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:29.397][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:29.398][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:29.399][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:29.400][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:29.401][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:29.403][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-04-26 16:04:29.403][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-04-26 16:04:29.404][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:29.405][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:29.406][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.407][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:29.409][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-04-26 16:04:29.411][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:29.412][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-04-26 16:04:29.413][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.414][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:29.415][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.417][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:29.418][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.419][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:29.420][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-26 16:04:29.421][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:29.423][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.424][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-04-26 16:04:29.425][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:29.426][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-04-26 16:04:29.426][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:29.426][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:29.426][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:29.426][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:29.426][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:29.426][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:29.426][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:29.426][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:29.426][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:29.426][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-04-26 16:04:29.426][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:29.426][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:29.426][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:29.428][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:29.429][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:29.429][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:04:29.429][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:04:29.430][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-04-26 16:04:29.431][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:29.432][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:29.433][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:29.435][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:29.436][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:29.437][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:29.438][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-04-26 16:04:29.438][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-04-26 16:04:29.438][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-04-26 16:04:29.439][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:29.440][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:29.441][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.443][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-04-26 16:04:29.444][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-04-26 16:04:29.446][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.447][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-04-26 16:04:29.449][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.450][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:29.451][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.452][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:29.453][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.455][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:29.456][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-26 16:04:29.457][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:29.458][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.459][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-04-26 16:04:29.461][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:29.462][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-04-26 16:04:29.462][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-04-26 16:04:29.463][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:29.464][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:29.465][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-04-26 16:04:29.467][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:29.468][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:29.469][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:29.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:29.471][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:29.472][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:29.473][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-04-26 16:04:29.473][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-04-26 16:04:29.473][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-04-26 16:04:29.475][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:29.476][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:29.477][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:29.478][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-04-26 16:04:29.479][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-04-26 16:04:29.481][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-26 16:04:29.483][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-26 16:04:29.485][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-04-26 16:04:29.486][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-26 16:04:29.488][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-04-26 16:04:29.495][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2025-04-26 16:04:29.496][super$initialize] Register connector ncbi.gene with the request scheduler
biodb.DEBUG[2025-04-26 16:04:29.498][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.gene.
biodb.DEBUG[2025-04-26 16:04:29.499][private$addConnectorRules] Create new rule for URL "www.ncbi.nlm.nih.gov" of connector "ncbi.gene".
biodb.DEBUG[2025-04-26 16:04:29.501][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:04:29.507][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:04:29.509][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.gene".
biodb.DEBUG[2025-04-26 16:04:29.511][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:04:29.512][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:04:29.572][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2025-04-26 16:04:29.578][biodb::testThat]
biodb.INFO [2025-04-26 16:04:29.579][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-04-26 16:04:29.580][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:29.581][biodb::testThat]
biodb.TRACE[2025-04-26 16:04:29.594][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2025-04-26 16:04:29.596][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:29.599][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-04-26 16:04:29.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:29.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.613][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:04:29.626][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:29.628][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:29.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.637][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:29.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:29.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.645][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:29.646][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:29.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.648][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.650][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:29.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:29.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.655][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:29.657][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:29.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.659][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.661][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:29.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:29.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.666][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:29.668][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:29.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.670][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.673][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:29.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:29.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.679][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:29.681][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:29.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.683][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.685][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:29.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:29.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.690][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:29.691][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:29.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.694][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.697][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:29.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:29.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.706][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:29.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:29.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.711][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:29.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:29.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.716][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:29.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:29.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:29.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:29.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.726][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:29.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:29.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:29.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:29.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:29.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:29.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:29.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:29.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:29.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:29.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:29.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:29.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:29.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:29.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:29.765][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2025-04-26 16:04:29.767][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:29.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:29.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.772][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:29.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:29.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.777][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:29.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:29.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.782][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:29.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:29.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.786][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:29.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:29.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:29.791][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-04-26 16:04:29.817][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-04-26 16:04:29.819][initialize] Register connector ncbi.ccds with the request scheduler
biodb.DEBUG[2025-04-26 16:04:29.820][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.ccds.
biodb.DEBUG[2025-04-26 16:04:29.835][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2025-04-26 16:04:29.837][self$recomputeFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:04:29.838][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2025-04-26 16:04:29.854][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:04:29.855][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:04:29.857][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2025-04-26 16:04:29.858][self$recomputeFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:04:29.859][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2025-04-26 16:04:29.861][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:04:29.862][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:04:29.874][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2025-04-26 16:04:29.875][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2025-04-26 16:04:29.877][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-26 16:04:29.881][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS14416.1".
biodb.TRACE[2025-04-26 16:04:29.882][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-26 16:04:29.928][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS14416.1.html".
biodb.DEBUG[2025-04-26 16:04:29.930][conn$getEntryContent] 1 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-04-26 16:04:29.932][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:29.933][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-04-26 16:04:29.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:29.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:29.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:29.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:29.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:29.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:29.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:29.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:29.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:29.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.968][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:29.969][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:29.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.972][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.974][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:29.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:29.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.979][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:29.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:29.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.984][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:29.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:29.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:29.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:29.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.993][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:29.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:29.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:29.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:29.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:30.063][self$createEntryFromContent] Accession numbers: CCDS14416.1.
biodb.TRACE[2025-04-26 16:04:30.064][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.069][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.074][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.079][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:30.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:30.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.084][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:30.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:30.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.089][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:30.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:30.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.093][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:30.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:30.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.124][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:30.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:30.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.165][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:30.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:30.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.175][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:30.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:30.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.180][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:30.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:30.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.208][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.209][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.211][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.227][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:30.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:30.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.232][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:30.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:30.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.237][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:30.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:30.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.242][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:30.243][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:30.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.245][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.246][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:30.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:30.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.261][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:30.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:30.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.267][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:30.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:30.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.271][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:30.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:30.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.276][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:30.278][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:30.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.280][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.281][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:30.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:30.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.301][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.307][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.311][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.316][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.317][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.320][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.321][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.336][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.341][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.346][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.350][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.352][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.354][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.355][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.372][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:30.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:30.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.377][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:30.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:30.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.382][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:30.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:30.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.386][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:30.388][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:30.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.390][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.391][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:30.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:30.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.406][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:30.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:30.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.411][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:30.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:30.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:30.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:30.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.426][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:30.427][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:30.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.430][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.431][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:30.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:30.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.446][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:30.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.451][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.456][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.461][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:30.462][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.464][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.465][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:30.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.480][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.482][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.484][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.491][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:30.492][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:30.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.495][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.501][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.503][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.505][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.512][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:30.513][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:30.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.515][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.522][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:30.524][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:30.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.526][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.533][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:30.534][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:30.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.536][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.543][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.545][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.547][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.559][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.560][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.562][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.563][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.581][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-3002-content.xml".
biodb.DEBUG[2025-04-26 16:04:30.582][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:30.584][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-04-26 16:04:30.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:30.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:30.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:30.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:30.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:30.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:30.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:30.611][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.612][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.615][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.622][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:30.623][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:30.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.626][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.628][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:30.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:30.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.633][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:30.634][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:30.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.636][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.639][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:30.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:30.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.644][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:30.645][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:30.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.647][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.650][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:30.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:30.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.655][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:30.656][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:30.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.658][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.661][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:30.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:30.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.666][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.667][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.669][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.674][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:30.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.684][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.689][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:30.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:30.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.694][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:30.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:30.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.704][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:30.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:30.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:30.744][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3002.
biodb.TRACE[2025-04-26 16:04:30.747][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.752][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.757][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.761][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.766][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:30.771][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-04-26 16:04:30.773][private$loadEntries] Creating entries from ids [1]: "CCDS9633.1".
biodb.DEBUG[2025-04-26 16:04:30.818][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-26 16:04:30.833][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS9633.1".
biodb.TRACE[2025-04-26 16:04:30.835][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-26 16:04:30.881][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS9633.1.html".
biodb.DEBUG[2025-04-26 16:04:30.883][conn$getEntryContent] 1 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-04-26 16:04:30.885][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:30.886][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-04-26 16:04:30.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:30.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:30.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:30.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:30.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:30.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:30.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:30.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.920][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:30.922][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.924][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.926][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:30.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.931][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.936][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.945][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:30.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:30.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:30.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:30.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:30.985][self$createEntryFromContent] Accession numbers: CCDS9633.1.
biodb.TRACE[2025-04-26 16:04:30.994][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:30.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:30.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.000][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.004][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.009][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:31.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:31.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.014][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:31.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:31.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.019][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:31.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:31.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.024][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:31.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:31.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.056][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.103][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.108][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.113][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.141][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.142][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.144][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.160][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:31.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:31.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.165][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:31.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:31.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.170][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:31.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:31.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.177][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:31.179][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:31.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.183][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.185][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:31.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:31.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.205][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:31.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:31.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.210][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:31.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:31.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.215][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:31.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:31.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.220][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:31.221][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:31.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.223][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.225][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:31.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:31.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.245][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.250][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.254][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.259][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.260][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.263][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.264][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.278][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.283][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.288][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.293][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.294][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.296][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.297][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.312][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:31.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:31.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.317][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:31.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:31.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.322][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:31.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:31.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.326][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:31.328][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:31.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.330][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.331][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:31.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:31.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.346][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:31.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:31.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.350][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:31.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:31.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:31.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:31.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.365][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:31.367][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:31.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.369][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.370][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:31.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:31.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.385][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:31.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.390][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.395][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.400][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:31.401][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.403][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.404][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:31.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.419][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.420][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.423][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.430][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:31.431][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:31.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.433][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.440][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.441][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.444][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.450][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:31.452][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:31.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.454][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.461][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:31.462][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:31.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.465][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.472][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:31.473][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:31.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.475][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.487][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.489][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.491][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.498][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.499][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.502][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.526][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-3627-content.xml".
biodb.DEBUG[2025-04-26 16:04:31.528][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:31.529][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-04-26 16:04:31.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:31.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:31.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:31.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:31.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:31.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:31.543][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:04:31.564][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.565][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.567][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.575][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:31.576][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:31.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.579][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.582][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:31.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:31.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.586][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:31.588][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:31.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.590][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.593][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:31.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:31.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.598][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:31.599][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:31.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.601][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.604][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:31.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:31.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.609][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:31.610][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:31.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.612][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.615][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:31.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:31.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.620][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.621][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.624][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.630][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:31.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.641][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.649][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.656][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.680][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:31.716][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3627.
biodb.TRACE[2025-04-26 16:04:31.718][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.723][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.728][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.732][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.737][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:31.742][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-04-26 16:04:31.743][private$loadEntries] Creating entries from ids [1]: "CCDS43240.1".
biodb.DEBUG[2025-04-26 16:04:31.744][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-26 16:04:31.746][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS43240.1".
biodb.TRACE[2025-04-26 16:04:31.748][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-26 16:04:31.751][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS43240.1.html".
biodb.DEBUG[2025-04-26 16:04:31.752][conn$getEntryContent] 1 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-04-26 16:04:31.754][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:31.755][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-04-26 16:04:31.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:31.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:31.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:31.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:31.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:31.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:31.769][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:04:31.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.787][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:31.789][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.791][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.793][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:31.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.798][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.808][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.818][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:31.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:31.852][self$createEntryFromContent] Accession numbers: CCDS43240.1.
biodb.TRACE[2025-04-26 16:04:31.853][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.858][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.863][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:31.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.868][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:31.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:31.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.873][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:31.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:31.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.878][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:31.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:31.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.882][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:31.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:31.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.914][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.961][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.965][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.970][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:31.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:31.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:31.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:31.998][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:31.999][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.002][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.018][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:32.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.023][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.028][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.033][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:32.034][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.036][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.037][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:32.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.052][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:32.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.057][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.068][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.073][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:32.074][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.076][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.077][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:32.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.092][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.097][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.102][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.107][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.108][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.110][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.112][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.126][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.131][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.136][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.141][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.142][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.145][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.146][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.161][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:32.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:32.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.166][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:32.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:32.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.171][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:32.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:32.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.175][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:32.177][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:32.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.179][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.185][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:32.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:32.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.201][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:32.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:32.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.206][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:32.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:32.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.211][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:32.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:32.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.216][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:32.217][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:32.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.219][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.221][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:32.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:32.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.236][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:32.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.241][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.246][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.251][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:32.252][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.254][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.256][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:32.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.271][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.272][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.275][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.282][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.283][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.285][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.292][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.293][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.296][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.303][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:32.304][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:32.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.306][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.319][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.320][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.322][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.323][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.329][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:32.331][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:32.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.333][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.340][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.341][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.343][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.350][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.352][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.354][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.372][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-4316-content.xml".
biodb.DEBUG[2025-04-26 16:04:32.374][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:32.376][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-04-26 16:04:32.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:32.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:32.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:32.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:32.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:32.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:32.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:32.404][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.405][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.408][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.415][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:32.416][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:32.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.418][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.421][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:32.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:32.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.426][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:32.427][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.429][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.432][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:32.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.437][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:32.438][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.439][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.440][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.443][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:32.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.448][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:32.449][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:32.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.451][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.454][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:32.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:32.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.459][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.460][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.463][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.471][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.479][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.484][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:32.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:32.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.489][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:32.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:32.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.499][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:32.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:32.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:32.533][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 4316.
biodb.TRACE[2025-04-26 16:04:32.535][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.540][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.545][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.550][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.555][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:32.559][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-04-26 16:04:32.561][private$loadEntries] Creating entries from ids [1]: "CCDS8317.1".
biodb.DEBUG[2025-04-26 16:04:32.562][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-26 16:04:32.564][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS8317.1".
biodb.TRACE[2025-04-26 16:04:32.566][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-26 16:04:32.611][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS8317.1.html".
biodb.DEBUG[2025-04-26 16:04:32.613][conn$getEntryContent] 1 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-04-26 16:04:32.615][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:32.616][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-04-26 16:04:32.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:32.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:32.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:32.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:32.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:32.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:32.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:32.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.657][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:32.658][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.660][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.662][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:32.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.667][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.672][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.684][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:32.718][self$createEntryFromContent] Accession numbers: CCDS8317.1.
biodb.TRACE[2025-04-26 16:04:32.719][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.724][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.729][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:32.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.734][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:32.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:32.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.739][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:32.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:32.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.743][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:32.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:32.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.748][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:32.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:32.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.785][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:32.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:32.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.827][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:32.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:32.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.832][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:32.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:32.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.837][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:32.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:32.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.865][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.866][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.868][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:32.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:32.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.884][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:32.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.889][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.894][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.906][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:32.907][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.910][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.911][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:32.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:32.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.926][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:32.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.931][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.936][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.941][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:32.942][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.944][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.946][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:32.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:32.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.960][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.966][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.970][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.975][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.977][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.979][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.980][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:32.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:32.995][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:32.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:32.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.000][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.005][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.010][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.011][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.012][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.013][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.015][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.035][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:33.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:33.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.041][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:33.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:33.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.045][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:33.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:33.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.050][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:33.052][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:33.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.054][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.055][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:33.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:33.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.070][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:33.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:33.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.075][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:33.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:33.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.080][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:33.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:33.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.085][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:33.086][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:33.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.088][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.089][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:33.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:33.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.104][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:33.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.109][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.114][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.119][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:33.120][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.123][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.124][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:33.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.139][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.140][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.142][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.155][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:33.156][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:33.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.159][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.166][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.167][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.170][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.176][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:33.178][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:33.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.180][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.187][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:33.188][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:33.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.190][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.197][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:33.199][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:33.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.201][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.210][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.212][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.214][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.221][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.222][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.225][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.259][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-50943-content.xml".
biodb.DEBUG[2025-04-26 16:04:33.261][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:33.263][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-04-26 16:04:33.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:33.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:33.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:33.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:33.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:33.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:33.277][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:04:33.310][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.311][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.314][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.323][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:33.324][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:33.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.327][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.331][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:33.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:33.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.336][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:33.337][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:33.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.339][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.344][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:33.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:33.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.348][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:33.350][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:33.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.357][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.362][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:33.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:33.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.367][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:33.369][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:33.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.371][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.375][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:33.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:33.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.380][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.382][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.384][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.392][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.405][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.410][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:33.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:33.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.415][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:33.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:33.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.425][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:33.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:33.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:33.459][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 50943.
biodb.TRACE[2025-04-26 16:04:33.461][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.466][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.471][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.476][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.481][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:33.485][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-04-26 16:04:33.487][private$loadEntries] Creating entries from ids [1]: "CCDS14323.1".
biodb.DEBUG[2025-04-26 16:04:33.488][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-26 16:04:33.495][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS14323.1".
biodb.TRACE[2025-04-26 16:04:33.497][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-26 16:04:33.546][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS14323.1.html".
biodb.DEBUG[2025-04-26 16:04:33.549][conn$getEntryContent] 1 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-04-26 16:04:33.550][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:33.552][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-04-26 16:04:33.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:33.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:33.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:33.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:33.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:33.565][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:33.566][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:04:33.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.591][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:33.593][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.595][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.597][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:33.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.602][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.607][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.616][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:33.650][self$createEntryFromContent] Accession numbers: CCDS14323.1.
biodb.TRACE[2025-04-26 16:04:33.651][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.656][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.660][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:33.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.670][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:33.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:33.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.678][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:33.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:33.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.682][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:33.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:33.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.687][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:33.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:33.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.716][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:33.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:33.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.756][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:33.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:33.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.761][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:33.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:33.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.766][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:33.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:33.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.793][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.794][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.797][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:33.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:33.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.819][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:33.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:33.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.823][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:33.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:33.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.828][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:33.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:33.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.833][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:33.834][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:33.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.837][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.838][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:33.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:33.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.853][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:33.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:33.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.857][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:33.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:33.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.862][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:33.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:33.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.867][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:33.868][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:33.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.871][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.872][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:33.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:33.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.887][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.892][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.896][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.901][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.902][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.905][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.906][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:33.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.921][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.931][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.936][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.941][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.942][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.944][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.946][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:33.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.960][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:33.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:33.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.965][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:33.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:33.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.970][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:33.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:33.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.974][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:33.976][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:33.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.978][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.979][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:33.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:33.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.994][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:33.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:33.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:33.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:33.999][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:34.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:34.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.003][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:34.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:34.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.008][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:34.010][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:34.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.012][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.013][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:34.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:34.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.028][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:34.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.033][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.038][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.042][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:34.048][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.051][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.053][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:34.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.068][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.069][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.071][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.072][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.079][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:34.081][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:34.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.084][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.095][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.098][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.101][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.112][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:34.115][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:34.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.118][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.129][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:34.131][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:34.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.135][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.144][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:34.145][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:34.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.147][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.154][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.156][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.158][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.165][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.166][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.168][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.184][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-5551-content.xml".
biodb.DEBUG[2025-04-26 16:04:34.186][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:34.187][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-04-26 16:04:34.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:34.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:34.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:34.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:34.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:34.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:34.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:34.212][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.214][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.216][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.229][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:34.230][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:34.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.233][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.235][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:34.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:34.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.239][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:34.241][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:34.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.243][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.245][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:34.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:34.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.250][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:34.251][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:34.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.253][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.255][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:34.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:34.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.260][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:34.262][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:34.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.264][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.266][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:34.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:34.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.271][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.272][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.274][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.277][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.284][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.288][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:34.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:34.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.293][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:34.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:34.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.303][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:34.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:34.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:34.336][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 5551.
biodb.TRACE[2025-04-26 16:04:34.339][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.349][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.355][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.360][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.365][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:34.369][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-04-26 16:04:34.371][private$loadEntries] Creating entries from ids [1]: "CCDS7305.1".
biodb.DEBUG[2025-04-26 16:04:34.372][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-26 16:04:34.374][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS7305.1".
biodb.TRACE[2025-04-26 16:04:34.375][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-26 16:04:34.421][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS7305.1.html".
biodb.DEBUG[2025-04-26 16:04:34.422][conn$getEntryContent] 1 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-04-26 16:04:34.424][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:34.426][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-04-26 16:04:34.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:34.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:34.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:34.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:34.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:34.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:34.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:34.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.464][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:34.466][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.468][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.470][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:34.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.475][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.480][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.490][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:34.530][self$createEntryFromContent] Accession numbers: CCDS7305.1.
biodb.TRACE[2025-04-26 16:04:34.531][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.536][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.541][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.546][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:34.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:34.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.551][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:34.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:34.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.555][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:34.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:34.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.560][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:34.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:34.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.592][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:34.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:34.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.638][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:34.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:34.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.643][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:34.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:34.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.648][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:34.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:34.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.683][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.684][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.686][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.703][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:34.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:34.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.708][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:34.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:34.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.713][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:34.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:34.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.718][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:34.720][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:34.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.722][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.723][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:34.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:34.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.739][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:34.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:34.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.744][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:34.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:34.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.749][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:34.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:34.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.754][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:34.755][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:34.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.757][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.758][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:34.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:34.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.773][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.778][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.783][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.794][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.795][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.798][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.799][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:34.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.814][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.819][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.824][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.829][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.830][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.832][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.834][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:34.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.848][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:34.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:34.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.853][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:34.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:34.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.858][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:34.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:34.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.863][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:34.864][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:34.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.866][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.868][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:34.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:34.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.882][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:34.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:34.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.887][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:34.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:34.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.892][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:34.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:34.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.897][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:34.898][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:34.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.900][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.902][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:34.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:34.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.922][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:34.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.927][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.932][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.937][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:34.938][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.941][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.942][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:34.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.957][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.958][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:34.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.960][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.967][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:34.968][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:34.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.970][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.977][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:34.978][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:34.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.981][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.987][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:34.989][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:34.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:34.991][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:34.997][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:34.999][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:35.000][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.001][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.008][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:35.009][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:35.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.011][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.018][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.019][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.021][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.028][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.029][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.032][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.052][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-916-content.xml".
biodb.DEBUG[2025-04-26 16:04:35.054][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:35.056][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-04-26 16:04:35.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:35.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:35.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:35.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:35.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:35.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:35.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:35.081][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.083][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.085][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.092][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:35.093][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:35.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.096][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.098][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:35.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:35.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.103][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:35.104][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:35.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.107][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.109][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:35.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:35.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.114][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:35.115][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:35.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.117][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.119][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:35.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:35.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.124][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:35.126][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:35.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.128][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.130][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:35.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:35.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.135][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.137][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.139][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.142][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.149][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.154][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:35.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:35.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.158][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:35.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:35.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.168][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:35.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:35.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:35.208][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 916.
biodb.TRACE[2025-04-26 16:04:35.211][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.216][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.221][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.226][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.231][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:35.236][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-04-26 16:04:35.237][private$loadEntries] Creating entries from ids [1]: "CCDS31685.1".
biodb.DEBUG[2025-04-26 16:04:35.238][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-26 16:04:35.240][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS31685.1".
biodb.TRACE[2025-04-26 16:04:35.242][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-26 16:04:35.287][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS31685.1.html".
biodb.DEBUG[2025-04-26 16:04:35.289][conn$getEntryContent] 1 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-04-26 16:04:35.291][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:35.293][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-04-26 16:04:35.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:35.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:35.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:35.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:35.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:35.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:35.307][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:04:35.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.327][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:35.329][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.331][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.333][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:35.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.338][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.342][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.358][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:35.392][self$createEntryFromContent] Accession numbers: CCDS31685.1.
biodb.TRACE[2025-04-26 16:04:35.394][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.398][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.403][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.408][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:35.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:35.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.413][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:35.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:35.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.418][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:35.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:35.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.423][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:35.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:35.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.452][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:35.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:35.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.500][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:35.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:35.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.505][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:35.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:35.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.509][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:35.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:35.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.538][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.539][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.541][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.557][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:35.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:35.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.562][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:35.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:35.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.567][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:35.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:35.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.572][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:35.573][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:35.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.576][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.577][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:35.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:35.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.592][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:35.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:35.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.597][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:35.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:35.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.602][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:35.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:35.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.612][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:35.614][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:35.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.616][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.618][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:35.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:35.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.632][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.637][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.642][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.647][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.648][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.651][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.652][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:35.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.667][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.672][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.677][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.682][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.683][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.686][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.687][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:35.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.702][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:35.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:35.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.707][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:35.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:35.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.711][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:35.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:35.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.716][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:35.717][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:35.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.720][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.721][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:35.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:35.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:35.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:35.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.747][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:35.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:35.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:35.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:35.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.757][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:35.758][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:35.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.761][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:35.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:35.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.777][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:35.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.782][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.787][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.791][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:35.793][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.795][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.796][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-04-26 16:04:35.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.811][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.813][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:35.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.815][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.822][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:35.823][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:35.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.826][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.832][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:35.834][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:35.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.836][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:35.843][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:35.844][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:35.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:35.846][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.007][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.009][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.011][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.018][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:36.019][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:36.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.022][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.028][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:36.029][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:36.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.032][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.038][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:36.040][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:36.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.042][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.050][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-9606-content.xml".
biodb.DEBUG[2025-04-26 16:04:36.052][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:36.054][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-04-26 16:04:36.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:36.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:36.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:36.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:36.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:36.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:36.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:36.071][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.073][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.075][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.081][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:36.083][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:36.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.085][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.086][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:36.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:36.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.091][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:36.092][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:36.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.095][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.096][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:36.097][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.099][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.101][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:36.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.106][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:36.107][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:36.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.109][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.110][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:36.112][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:36.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.114][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.115][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.120][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.129][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:36.164][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 9606.
biodb.TRACE[2025-04-26 16:04:36.167][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:36.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:36.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.172][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:36.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:36.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.178][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:36.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:36.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.183][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:36.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:36.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.188][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:36.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:36.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.194][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:36.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:36.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.199][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:36.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:36.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.230][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.276][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.281][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.286][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.317][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.318][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.321][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.339][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:36.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.345][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.350][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.355][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:36.357][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.359][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.361][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:36.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.377][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:36.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:36.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.382][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:36.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:36.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.388][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:36.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:36.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.393][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:36.395][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:36.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.397][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.398][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:36.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:36.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.415][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.416][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.419][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.426][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:36.427][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:36.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.430][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.438][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.439][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.442][ef$get] fields variable is a list.
biodb.INFO [2025-04-26 16:04:36.455][biodb::testThat]
biodb.INFO [2025-04-26 16:04:36.456][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-26 16:04:36.458][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:36.459][biodb::testThat]
biodb.DEBUG[2025-04-26 16:04:36.462][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2025-04-26 16:04:36.464][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
biodb.TRACE[2025-04-26 16:04:36.466][cch$loadFileContent] Trying to load 8 files from cache: [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.TRACE[2025-04-26 16:04:36.469][cch$loadFileContent] file.exist = [8]: "TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE".
biodb.TRACE[2025-04-26 16:04:36.711][loadFileContents] Loaded 8 files from cache: [8]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/2833.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/3002.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/3627.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/4316.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/50943.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/5551.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/916.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/9606.xml".
biodb.DEBUG[2025-04-26 16:04:36.713][conn$getEntryContent] 8 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-04-26 16:04:36.714][self$createEntryFromContent] Creating NCBI Gene entries from 8 content(s).
biodb.DEBUG[2025-04-26 16:04:36.716][self$createEntryFromContent] Parsing 8 NCBI Gene entries.
biodb.DEBUG[2025-04-26 16:04:36.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:36.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:36.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:36.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:36.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:36.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:36.732][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:04:36.747][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.749][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.751][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.759][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:36.766][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:36.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.768][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.770][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:36.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:36.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.775][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:36.776][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:36.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.779][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.781][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:36.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:36.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.786][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:36.787][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.789][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.792][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:36.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.796][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:36.798][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:36.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.800][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.802][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:36.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:36.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.807][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:36.808][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:36.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.810][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.814][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:36.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:36.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.823][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:36.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:36.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.828][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.832][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.842][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:36.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:36.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:36.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:36.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:36.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:36.873][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:36.874][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:04:36.887][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.888][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.891][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.898][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:36.899][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:36.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.901][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.904][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:36.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:36.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.909][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:36.910][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:36.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.912][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.915][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:36.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:36.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.920][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:36.921][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.923][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.926][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:36.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:36.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.931][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:36.932][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:36.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.934][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.937][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:36.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:36.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.942][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:36.943][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:36.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.945][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.949][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:36.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:36.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.957][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:36.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:36.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.963][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.967][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.977][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:36.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:36.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:36.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:36.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:36.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:36.997][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:36.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:36.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:37.006][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:37.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:37.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:37.010][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:04:37.033][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.034][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.037][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.045][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:37.046][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:37.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.048][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.052][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:37.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:37.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.057][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:37.058][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:37.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.060][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.064][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:37.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:37.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.069][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:37.070][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:37.071][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.072][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.075][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:37.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:37.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.080][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:37.082][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:37.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.084][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.087][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:37.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:37.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.092][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.093][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.096][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.102][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.111][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:37.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:37.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.116][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.121][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.131][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:37.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:37.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:37.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:37.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:37.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:37.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:37.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:37.180][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.181][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.183][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.191][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:37.193][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:37.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.195][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.198][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:37.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:37.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.203][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:37.204][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:37.205][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.206][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.209][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:37.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:37.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.214][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:37.215][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:37.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.218][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.220][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:37.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:37.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.225][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:37.226][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:37.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.229][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.231][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:37.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:37.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.236][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.238][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.240][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.244][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.251][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:37.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:37.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.256][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.261][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.270][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:37.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:37.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:37.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:37.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:37.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:37.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:37.307][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:04:37.340][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.342][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.343][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.344][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.354][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:37.355][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:37.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.357][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.362][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:37.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:37.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.366][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:37.368][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:37.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.370][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.374][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:37.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:37.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.379][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:37.380][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:37.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.383][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.387][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:37.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:37.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.392][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:37.393][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:37.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.396][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.400][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:37.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:37.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.405][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.406][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.408][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.417][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.431][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:37.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:37.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.436][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.441][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.450][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:37.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:37.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:37.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:37.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:37.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:37.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:37.482][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:04:37.494][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.495][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.497][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.505][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:37.506][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:37.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.508][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.511][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:37.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:37.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.516][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:37.517][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:37.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.519][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.522][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:37.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:37.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.526][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:37.528][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:37.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.530][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.532][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:37.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:37.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.537][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:37.538][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:37.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.541][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.543][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:37.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:37.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.548][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.549][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.551][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.555][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.562][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:37.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:37.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.567][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.571][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.581][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:37.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:37.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:37.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:37.609][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:37.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:37.611][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:37.612][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:04:37.623][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.625][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.627][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.634][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:37.636][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:37.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.638][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.640][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:37.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:37.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.645][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:37.646][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:37.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.649][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.651][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:37.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:37.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.656][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:37.657][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:37.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.659][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.662][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:37.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:37.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.666][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:37.668][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:37.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.670][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.672][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:37.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:37.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.678][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.680][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.683][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.688][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.695][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:37.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:37.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.700][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.704][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.714][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:37.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:37.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:37.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:37.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:37.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:37.745][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:37.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:37.748][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.750][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.752][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.759][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:37.760][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:37.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.762][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.764][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-26 16:04:37.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-26 16:04:37.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.769][ef$get] Asked field names are: location.
biodb.TRACE[2025-04-26 16:04:37.770][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-04-26 16:04:37.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.772][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.773][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:37.775][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:37.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.777][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.778][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-04-26 16:04:37.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-04-26 16:04:37.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.783][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-04-26 16:04:37.785][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:37.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.787][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.788][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.790][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-04-26 16:04:37.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.792][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.794][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.798][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.808][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-04-26 16:04:37.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:37.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:37.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:37.946][self$createEntryFromContent] Accession numbers: 2833, 3002, 3627, 4316, 50943, 5551, 916, 9606.
biodb.TRACE[2025-04-26 16:04:37.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:37.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:37.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:37.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:37.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:37.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:37.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:37.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:37.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:37.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:37.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:37.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:37.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:37.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:37.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:37.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:37.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:37.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:37.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:38.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:38.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:38.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:38.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:38.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:38.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:38.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:38.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:38.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:38.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:38.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:38.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:38.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:38.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:38.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:38.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.060][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:38.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:38.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:38.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:38.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:38.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:38.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:38.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:38.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:38.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:38.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:38.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:04:38.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:38.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:04:38.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:38.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:04:38.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-26 16:04:38.135][biodb::testThat]
biodb.INFO [2025-04-26 16:04:38.137][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-26 16:04:38.138][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:38.139][biodb::testThat]
biodb.TRACE[2025-04-26 16:04:38.142][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:38.144][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:38.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.146][ef$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:38.148][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.TRACE[2025-04-26 16:04:38.166][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:38.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:38.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.171][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:38.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:38.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.176][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:38.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:38.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:38.184][function(conn, opt)] With value "GPR9".
biodb.DEBUG[2025-04-26 16:04:38.192][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term="GPR9"[Gene Name]&retmax=1".
biodb.DEBUG[2025-04-26 16:04:38.211][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-26 16:04:38.212][cch$loadFileContent] Trying to load 1 files from cache: [1]: "21e81c63f052370fa801f15c9311a3f4".
biodb.TRACE[2025-04-26 16:04:38.214][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-26 16:04:38.230][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/21e81c63f052370fa801f15c9311a3f4.content".
biodb.DEBUG[2025-04-26 16:04:38.232][function(conn, opt)] With found IDs [1]: "2833".
biodb.INFO [2025-04-26 16:04:38.256][biodb::testThat]
biodb.INFO [2025-04-26 16:04:38.257][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-04-26 16:04:38.259][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:38.260][biodb::testThat]
biodb.TRACE[2025-04-26 16:04:38.276][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:38.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:38.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.281][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:38.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:38.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.286][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:38.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:38.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:38.337][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term="GPR9"[Gene Name]&retmax=1".
biodb.DEBUG[2025-04-26 16:04:38.341][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-26 16:04:38.343][cch$loadFileContent] Trying to load 1 files from cache: [1]: "21e81c63f052370fa801f15c9311a3f4".
biodb.TRACE[2025-04-26 16:04:38.345][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-26 16:04:38.347][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/21e81c63f052370fa801f15c9311a3f4.content".
biodb.INFO [2025-04-26 16:04:38.371][biodb::testThat]
biodb.INFO [2025-04-26 16:04:38.373][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-04-26 16:04:38.374][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:38.375][biodb::testThat]
biodb.TRACE[2025-04-26 16:04:38.389][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:38.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:38.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.394][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:38.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:38.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.399][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:38.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:38.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.404][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:38.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:38.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.408][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:38.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:38.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:38.413][private$computeField] Compute value for field "aa.seq".
biodb.TRACE[2025-04-26 16:04:38.414][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:38.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:38.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.419][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:38.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:38.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.424][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:38.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:38.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.429][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:38.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:38.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.434][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:38.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:38.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.439][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:38.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:38.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.444][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:38.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:38.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.450][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:38.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:38.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.455][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:38.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:38.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.460][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:38.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:38.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.465][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:38.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:38.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.469][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:38.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:38.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:38.474][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:38.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:38.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:38.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-26 16:04:38.499][biodb::testThat]
biodb.INFO [2025-04-26 16:04:38.500][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-26 16:04:38.501][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:38.503][biodb::testThat]
biodb.INFO [2025-04-26 16:04:38.517][biodb::testThat]
biodb.INFO [2025-04-26 16:04:38.518][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-26 16:04:38.520][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:38.521][biodb::testThat]
biodb.INFO [2025-04-26 16:04:38.532][biodb::testThat]
biodb.INFO [2025-04-26 16:04:38.533][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-26 16:04:38.534][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:38.535][biodb::testThat]
biodb.DEBUG[2025-04-26 16:04:38.540][function(conn, opt)] Trying to download "https://www.ncbi.nlm.nih.gov/gene?term=2833".
biodb.DEBUG[2025-04-26 16:04:41.634][getUrlContent] Use RCurl for downloading content of URL https://www.ncbi.nlm.nih.gov/gene?term=2833.
biodb.INFO [2025-04-26 16:04:44.698][biodb::testThat]
biodb.INFO [2025-04-26 16:04:44.700][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-26 16:04:44.701][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:44.702][biodb::testThat]
biodb.INFO [2025-04-26 16:04:44.711][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-26 16:04:44.713][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.gene from the request scheduler
biodb.INFO [2025-04-26 16:04:44.714][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.DEBUG[2025-04-26 16:04:44.716][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.ccds from the request scheduler
biodb.INFO [2025-04-26 16:04:44.723][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-04-26 16:04:44.724][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-26 16:04:44.725][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:44.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:44.728][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:44.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:44.730][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-26 16:04:44.736][biodb::testContext]
biodb.INFO [2025-04-26 16:04:44.738][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:04:44.739][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2025-04-26 16:04:44.740][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:04:44.741][biodb::testContext]
biodb.INFO [2025-04-26 16:04:44.744][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-26 16:04:44.746][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-26 16:04:44.752][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:04:44.753][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-26 16:04:44.754][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-26 16:04:44.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:44.759][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-26 16:04:44.760][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-26 16:04:44.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:44.764][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-26 16:04:44.766][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-26 16:04:44.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:44.770][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-26 16:04:44.771][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-26 16:04:44.772][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-26 16:04:44.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:44.777][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-26 16:04:44.778][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-26 16:04:44.779][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-26 16:04:44.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:44.784][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-26 16:04:44.785][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-26 16:04:44.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:44.789][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-26 16:04:44.790][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-26 16:04:44.792][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-26 16:04:44.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:44.796][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-26 16:04:44.797][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-26 16:04:44.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:44.802][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-26 16:04:44.803][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-26 16:04:44.804][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-26 16:04:44.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.807][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[2025-04-26 16:04:44.809][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:04:44.810][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-26 16:04:44.811][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-26 16:04:44.812][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-26 16:04:44.813][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-26 16:04:44.815][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-26 16:04:44.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:44.819][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-26 16:04:44.820][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-26 16:04:44.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:44.825][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-26 16:04:44.826][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-26 16:04:44.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:44.831][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-26 16:04:44.832][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-26 16:04:44.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:44.836][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-26 16:04:44.837][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-26 16:04:44.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:44.842][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-26 16:04:44.843][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-26 16:04:44.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.846][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[2025-04-26 16:04:44.848][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:04:44.849][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-26 16:04:44.852][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-26 16:04:44.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:44.856][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-26 16:04:44.858][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-26 16:04:44.859][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-26 16:04:44.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:44.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:44.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:44.864][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-26 16:04:44.866][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:44.867][self$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[2025-04-26 16:04:44.868][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.870][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:44.871][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.872][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:44.873][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:44.874][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:44.876][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:04:44.877][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:44.878][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.879][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-26 16:04:44.886][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:44.889][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:44.890][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.891][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:44.891][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:04:44.891][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:04:44.891][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:04:44.891][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:04:44.893][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:44.894][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:44.895][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:44.896][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:44.897][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:44.898][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:44.899][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:44.900][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:44.902][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:44.903][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:44.904][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:44.905][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:44.906][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-26 16:04:44.908][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:44.909][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:04:44.911][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.912][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:44.913][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.914][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:44.915][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:44.917][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:44.918][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:04:44.919][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:44.920][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.921][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-26 16:04:44.922][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:44.924][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:44.925][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.926][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:44.926][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:04:44.926][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:04:44.926][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:04:44.926][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:04:44.927][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:44.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:44.929][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:44.930][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:44.932][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:44.933][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:44.934][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:44.935][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:44.937][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:44.938][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:44.939][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:44.940][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:44.941][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-26 16:04:44.943][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.945][self$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[2025-04-26 16:04:44.946][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.947][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:44.948][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.949][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:44.951][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:44.952][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:44.953][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:04:44.954][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:44.955][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:44.956][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-26 16:04:44.958][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:44.959][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:44.960][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.961][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:44.962][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:44.964][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:44.965][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:44.966][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:44.967][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:44.968][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:44.969][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:44.970][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:44.971][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:44.973][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:44.974][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:44.975][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:44.976][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-26 16:04:44.978][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.979][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:04:44.980][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.982][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:44.983][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.984][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:44.985][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:44.986][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:44.987][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:04:44.989][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:44.990][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:44.991][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-26 16:04:44.992][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:44.993][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:44.994][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:44.996][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:44.997][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:44.998][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:44.999][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:45.000][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:45.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:45.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:45.004][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:45.005][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:45.006][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:45.007][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:45.008][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:45.009][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:45.011][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:04:45.012][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.030][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[2025-04-26 16:04:45.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.040][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[2025-04-26 16:04:45.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.046][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[2025-04-26 16:04:45.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.056][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[2025-04-26 16:04:45.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.062][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[2025-04-26 16:04:45.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.099][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[2025-04-26 16:04:45.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.106][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-26 16:04:45.108][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-26 16:04:45.109][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-26 16:04:45.111][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-26 16:04:45.112][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-26 16:04:45.114][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-26 16:04:45.115][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-26 16:04:45.117][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-26 16:04:45.118][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-26 16:04:45.120][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-26 16:04:45.121][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-26 16:04:45.123][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-26 16:04:45.125][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-26 16:04:45.126][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-26 16:04:45.128][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-26 16:04:45.129][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-26 16:04:45.131][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-26 16:04:45.132][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-26 16:04:45.134][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-26 16:04:45.135][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-26 16:04:45.137][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-26 16:04:45.138][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-26 16:04:45.140][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-26 16:04:45.141][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-26 16:04:45.143][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-26 16:04:45.144][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-26 16:04:45.146][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-26 16:04:45.148][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-26 16:04:45.149][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-26 16:04:45.151][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-26 16:04:45.152][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-26 16:04:45.154][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-26 16:04:45.155][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-26 16:04:45.157][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-26 16:04:45.158][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-26 16:04:45.160][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-26 16:04:45.162][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-26 16:04:45.163][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-26 16:04:45.165][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-26 16:04:45.166][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-26 16:04:45.168][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-26 16:04:45.169][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-26 16:04:45.171][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-26 16:04:45.172][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-26 16:04:45.174][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-26 16:04:45.176][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-26 16:04:45.177][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-26 16:04:45.179][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-26 16:04:45.180][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-26 16:04:45.182][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-26 16:04:45.183][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-26 16:04:45.185][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-26 16:04:45.186][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-26 16:04:45.188][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-26 16:04:45.190][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-26 16:04:45.191][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-26 16:04:45.193][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-26 16:04:45.194][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-26 16:04:45.196][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-26 16:04:45.197][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-26 16:04:45.199][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-26 16:04:45.200][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-26 16:04:45.202][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-26 16:04:45.204][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-26 16:04:45.205][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-26 16:04:45.207][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-26 16:04:45.208][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-26 16:04:45.210][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-26 16:04:45.211][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-26 16:04:45.213][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-26 16:04:45.214][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-26 16:04:45.216][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-26 16:04:45.218][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-26 16:04:45.219][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-26 16:04:45.221][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-26 16:04:45.222][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-26 16:04:45.224][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-26 16:04:45.225][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-26 16:04:45.227][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-26 16:04:45.228][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-26 16:04:45.230][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-26 16:04:45.231][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-26 16:04:45.233][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-26 16:04:45.235][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-26 16:04:45.237][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-26 16:04:45.238][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:04:45.239][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.241][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.250][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[2025-04-26 16:04:45.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.258][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[2025-04-26 16:04:45.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.294][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[2025-04-26 16:04:45.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.346][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[2025-04-26 16:04:45.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:45.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:45.379][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-04-26 16:04:45.381][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-04-26 16:04:45.383][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.384][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-04-26 16:04:45.385][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.387][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:45.388][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.389][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:45.390][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.391][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:45.392][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-04-26 16:04:45.394][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:45.395][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.396][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-04-26 16:04:45.397][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:45.398][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-04-26 16:04:45.398][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-04-26 16:04:45.400][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:45.401][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:45.402][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-26 16:04:45.403][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:45.404][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:45.405][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:45.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:45.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:45.409][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:45.410][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-04-26 16:04:45.410][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-04-26 16:04:45.411][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:45.412][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:45.413][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.414][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:45.416][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-04-26 16:04:45.418][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.419][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-04-26 16:04:45.420][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.421][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:45.423][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.424][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:45.425][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.426][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:45.427][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-26 16:04:45.429][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:45.430][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.431][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-04-26 16:04:45.432][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:45.433][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-04-26 16:04:45.433][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-04-26 16:04:45.433][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-04-26 16:04:45.433][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-04-26 16:04:45.433][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-04-26 16:04:45.433][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-04-26 16:04:45.435][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:45.436][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:45.437][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-26 16:04:45.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:45.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:45.440][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:45.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:45.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:45.444][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:45.445][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-04-26 16:04:45.445][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-04-26 16:04:45.446][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:45.447][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:45.448][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.450][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:45.451][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-04-26 16:04:45.453][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:45.454][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-04-26 16:04:45.456][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.457][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:45.458][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.459][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:45.460][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.461][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:45.463][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-26 16:04:45.464][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:45.465][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.466][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-04-26 16:04:45.467][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:45.469][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-04-26 16:04:45.469][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:45.469][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:45.469][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:45.469][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:45.469][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:45.469][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:45.469][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:45.469][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:45.469][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:45.469][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-04-26 16:04:45.469][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:45.469][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:45.469][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:45.470][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:45.471][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:45.471][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:04:45.471][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:04:45.472][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-04-26 16:04:45.474][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:45.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:45.476][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:45.477][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:45.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:45.479][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:45.480][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-04-26 16:04:45.480][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-04-26 16:04:45.480][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-04-26 16:04:45.482][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:45.483][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:45.484][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.485][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-04-26 16:04:45.486][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-04-26 16:04:45.488][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.490][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-04-26 16:04:45.491][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.492][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:45.493][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.494][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:45.495][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.497][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:45.498][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-26 16:04:45.499][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:45.500][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.501][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-04-26 16:04:45.503][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:45.504][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-04-26 16:04:45.504][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-04-26 16:04:45.505][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:45.506][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:45.507][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-04-26 16:04:45.508][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:45.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:45.511][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:45.512][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:45.513][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:45.514][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:45.515][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-04-26 16:04:45.515][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-04-26 16:04:45.515][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-04-26 16:04:45.516][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:45.517][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:45.519][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:45.520][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-04-26 16:04:45.521][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-04-26 16:04:45.523][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-26 16:04:45.525][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-26 16:04:45.527][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-04-26 16:04:45.528][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-26 16:04:45.530][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-04-26 16:04:45.537][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2025-04-26 16:04:45.539][super$initialize] Register connector ncbi.pubchem.comp with the request scheduler
biodb.DEBUG[2025-04-26 16:04:45.540][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.pubchem.comp.
biodb.DEBUG[2025-04-26 16:04:45.542][private$addConnectorRules] Create new rule for URL "pubchem.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.comp".
biodb.DEBUG[2025-04-26 16:04:45.543][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-04-26 16:04:45.544][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-04-26 16:04:45.546][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.comp".
biodb.DEBUG[2025-04-26 16:04:45.548][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-04-26 16:04:45.549][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-04-26 16:04:45.550][rule$addConnector] Connector "ncbi.pubchem.comp" is already listed in rule "pubchem.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-04-26 16:04:45.555][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2025-04-26 16:04:45.561][biodb::testThat]
biodb.INFO [2025-04-26 16:04:45.562][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-04-26 16:04:45.563][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:45.565][biodb::testThat]
biodb.TRACE[2025-04-26 16:04:45.569][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2025-04-26 16:04:45.570][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:45.574][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-04-26 16:04:45.575][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:45.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:45.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:45.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:45.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:45.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:45.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:45.593][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.594][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.597][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.603][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:45.604][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:45.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.607][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.608][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:45.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:45.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.613][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:45.615][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:45.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.617][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.618][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:45.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:45.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.623][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:45.625][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:45.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.627][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.629][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:45.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:45.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.633][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:45.635][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:45.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.637][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.639][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:45.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:45.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.643][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:45.645][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:45.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.647][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.649][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:45.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:45.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.653][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-04-26 16:04:45.655][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:45.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.657][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.659][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-04-26 16:04:45.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:45.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.664][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:45.665][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:45.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.667][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.669][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:45.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:45.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.675][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:45.677][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:45.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.680][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:45.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:45.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.687][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:45.688][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:45.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.690][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.692][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:45.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:45.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.697][ef$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:45.698][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:45.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.700][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.702][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:45.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:45.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.713][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-04-26 16:04:45.715][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:45.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.717][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-04-26 16:04:45.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:45.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.723][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:45.724][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:45.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.726][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.728][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:45.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:45.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.733][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:45.734][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:45.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.736][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.738][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:45.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:45.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.743][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-04-26 16:04:45.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:45.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.747][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:45.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:45.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.752][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:45.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:45.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.757][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-04-26 16:04:45.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:45.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.762][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:45.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:45.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.766][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:45.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:45.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.771][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-04-26 16:04:45.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:45.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.776][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:45.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:45.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.781][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:45.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:45.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.786][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-04-26 16:04:45.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:45.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.790][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:45.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:45.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.795][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:45.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:45.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.800][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-04-26 16:04:45.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:45.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.804][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:45.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:45.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.809][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:45.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:45.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:45.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:45.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.819][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:45.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:45.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.824][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:45.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:45.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.833][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:45.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:45.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:45.867][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2025-04-26 16:04:45.870][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:45.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:45.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.875][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:45.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:45.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.880][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:45.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:45.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.884][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:45.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:45.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.889][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:45.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:45.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.894][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:45.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:45.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.899][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:45.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:45.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.930][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:45.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:45.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.971][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:45.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:45.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.976][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:45.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:45.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.981][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:45.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:45.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:45.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:45.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:45.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:45.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:46.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:46.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:46.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:46.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.008][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:46.010][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:46.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.012][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:46.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:46.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.028][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-04-26 16:04:46.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:46.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:46.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:46.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:46.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:46.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.042][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-04-26 16:04:46.044][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:46.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.046][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.047][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-04-26 16:04:46.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:46.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-04-26 16:04:46.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:46.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:46.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:46.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:46.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:46.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.077][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-04-26 16:04:46.078][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:46.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.080][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-04-26 16:04:46.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:46.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.097][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:46.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:46.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.102][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:46.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:46.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.106][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:46.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:46.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.111][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:46.112][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:46.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.115][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.116][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:46.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:46.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.131][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:46.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:46.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.136][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:46.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:46.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.146][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:46.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:46.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.151][ef$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:46.153][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:46.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.155][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.156][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:46.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:46.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.171][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.176][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.181][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.185][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.186][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.189][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.190][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.205][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.210][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.214][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.219][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.220][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.223][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.224][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.238][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.243][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.248][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.253][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.254][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.256][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.257][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.272][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.277][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.282][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.286][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.288][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.290][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.291][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.306][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.311][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.316][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.321][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.322][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.324][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.326][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.340][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.345][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.350][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.355][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.356][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.358][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.359][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.374][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.379][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.384][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.389][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.391][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.393][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.394][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.409][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:46.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:46.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:46.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:46.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.419][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:46.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:46.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.424][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:46.425][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:46.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.427][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.428][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:46.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:46.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.443][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.448][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.453][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.458][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.459][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.461][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.463][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.478][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:46.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:46.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.483][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:46.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:46.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.488][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:46.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:46.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.493][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:46.494][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:46.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.496][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:46.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:46.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.513][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:46.514][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:46.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.516][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.523][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.525][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.527][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.534][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.535][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.538][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.545][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.546][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.549][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.556][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.557][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.559][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.566][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.568][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.570][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.577][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:46.584][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:46.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.586][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.593][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:46.595][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:46.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.597][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.604][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.605][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.607][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.614][ef$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:46.615][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:46.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.618][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.625][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:46.626][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:46.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.628][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.635][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:46.636][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:46.638][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.639][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.646][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:46.647][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:46.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.649][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.656][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.658][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.660][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.667][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.668][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.671][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.688][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2025-04-26 16:04:46.690][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:46.693][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-04-26 16:04:46.695][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:46.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:46.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:46.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:46.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:46.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:46.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:46.712][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:46.713][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:46.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.715][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:46.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:46.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.722][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.723][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.725][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.727][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.732][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.733][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.735][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.737][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.742][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.743][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.746][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.747][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.752][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.754][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.756][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.757][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.762][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.763][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.766][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.767][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.772][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-04-26 16:04:46.773][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:46.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.776][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.777][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-04-26 16:04:46.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:46.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.782][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:46.784][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:46.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.786][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.787][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:46.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:46.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.792][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:46.793][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:46.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.796][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.797][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:46.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:46.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.802][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.803][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.806][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:46.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.812][ef$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:46.813][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:46.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.816][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.817][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:46.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:46.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.822][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-04-26 16:04:46.823][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:46.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.826][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-04-26 16:04:46.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:46.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.832][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.834][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.836][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.837][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:46.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.842][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.844][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.846][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.848][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:46.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.853][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-04-26 16:04:46.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.858][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.863][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:46.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.867][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-04-26 16:04:46.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.872][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.877][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:46.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.882][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-04-26 16:04:46.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.886][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.891][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:46.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.896][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-04-26 16:04:46.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.901][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.906][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:46.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.910][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-04-26 16:04:46.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.915][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.920][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:46.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.925][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:46.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:46.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.930][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:46.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:46.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.934][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:46.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:46.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:46.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:46.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.944][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:46.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:46.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:46.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:46.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:46.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:46.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:46.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:46.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:46.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:46.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:46.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:46.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:46.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:46.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:46.977][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2025-04-26 16:04:46.980][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:46.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:46.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.985][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:46.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:46.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.989][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:46.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:46.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.994][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:46.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:46.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:46.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:46.999][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:47.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:47.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.004][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:47.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:47.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.009][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:47.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:47.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.044][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.085][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.090][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.095][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.122][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.124][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.126][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:47.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:47.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:47.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:47.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:47.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:47.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.156][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:47.157][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:47.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.159][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:47.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:47.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:47.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:47.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:47.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:47.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:47.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:47.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.190][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:47.191][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:47.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.194][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:47.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:47.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.209][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:47.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:47.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.214][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:47.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:47.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.219][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:47.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:47.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.224][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:47.225][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:47.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.227][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.229][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:47.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:47.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.243][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:47.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:47.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.248][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:47.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:47.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.253][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:47.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:47.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.258][ef$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:47.259][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:47.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.261][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.263][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:47.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:47.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.278][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:47.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:47.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.283][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:47.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:47.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.287][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:47.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:47.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.292][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:47.294][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:47.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.296][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.297][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:47.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:47.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.312][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:47.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:47.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.317][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:47.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:47.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.322][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:47.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:47.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.327][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:47.328][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:47.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.330][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.331][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:47.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:47.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:47.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:47.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.351][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:47.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:47.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.356][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:47.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:47.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.361][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:47.363][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:47.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.365][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:47.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:47.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:47.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:47.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.386][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:47.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:47.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.391][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:47.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:47.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.396][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:47.397][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:47.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.400][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:47.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:47.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.416][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:47.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:47.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.421][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:47.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:47.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.426][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:47.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:47.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.430][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:47.432][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:47.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.434][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.435][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:47.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:47.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.450][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:47.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:47.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.455][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:47.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:47.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.460][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:47.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:47.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.470][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:47.472][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:47.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.474][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.475][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:47.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:47.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.489][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:47.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:47.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.494][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:47.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:47.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.499][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:47.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:47.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.504][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:47.505][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:47.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.507][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.509][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:47.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:47.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.523][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:47.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:47.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.528][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:47.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:47.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.533][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:47.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:47.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.537][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:47.539][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:47.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.541][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.542][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:47.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:47.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.557][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:47.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:47.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.561][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:47.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:47.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.566][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:47.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:47.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.571][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:47.572][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:47.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.574][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.576][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:47.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:47.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:47.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:47.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.595][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:47.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:47.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.599][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:47.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:47.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.604][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:47.606][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:47.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.608][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.609][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:47.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:47.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.624][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.625][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.627][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.634][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:47.636][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-04-26 16:04:47.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.638][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.645][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:47.646][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-04-26 16:04:47.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.648][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.655][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:47.656][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-04-26 16:04:47.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.659][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.665][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:47.667][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-26 16:04:47.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.669][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.677][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:47.678][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-26 16:04:47.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.680][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.687][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:04:47.688][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:04:47.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.691][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.697][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:04:47.699][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:04:47.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.701][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.708][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:04:47.709][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:04:47.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.711][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.718][ef$get] Asked field names are: logp.
biodb.TRACE[2025-04-26 16:04:47.720][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-04-26 16:04:47.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.722][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.729][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:47.730][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:47.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.732][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.739][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:47.740][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-26 16:04:47.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.743][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.749][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:47.751][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:47.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.753][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.760][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:47.761][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-04-26 16:04:47.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.763][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.770][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:47.771][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-04-26 16:04:47.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.774][ef$get] fields variable is a list.
biodb.INFO [2025-04-26 16:04:47.786][biodb::testThat]
biodb.INFO [2025-04-26 16:04:47.787][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-26 16:04:47.788][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:47.789][biodb::testThat]
biodb.DEBUG[2025-04-26 16:04:47.792][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-04-26 16:04:47.794][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
biodb.TRACE[2025-04-26 16:04:47.797][cch$loadFileContent] Trying to load 2 files from cache: [2]: "2, 65124".
biodb.TRACE[2025-04-26 16:04:47.799][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-04-26 16:04:47.802][loadFileContents] Loaded 2 files from cache: [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/2.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/65124.xml".
biodb.DEBUG[2025-04-26 16:04:47.803][conn$getEntryContent] 2 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-04-26 16:04:47.805][self$createEntryFromContent] Creating PubChem Compound entries from 2 content(s).
biodb.DEBUG[2025-04-26 16:04:47.806][self$createEntryFromContent] Parsing 2 PubChem Compound entries.
biodb.DEBUG[2025-04-26 16:04:47.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:47.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:47.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:47.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:47.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:47.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:47.821][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.TRACE[2025-04-26 16:04:47.823][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.827][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:47.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:47.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:47.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:47.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:47.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:47.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:47.849][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:04:47.851][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.856][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:47.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:47.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:47.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:47.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:47.920][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2025-04-26 16:04:47.921][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-04-26 16:04:47.937][biodb::testThat]
biodb.INFO [2025-04-26 16:04:47.938][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-26 16:04:47.939][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:47.941][biodb::testThat]
biodb.TRACE[2025-04-26 16:04:47.944][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:47.945][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:47.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:47.947][ef$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:47.949][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.INFO [2025-04-26 16:04:48.181][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.182][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-04-26 16:04:48.184][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:48.185][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.227][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.229][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-04-26 16:04:48.230][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:48.231][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.271][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.272][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-26 16:04:48.273][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:48.275][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.291][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.292][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-26 16:04:48.293][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:48.294][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.307][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.308][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-26 16:04:48.309][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:48.310][biodb::testThat]
biodb.DEBUG[2025-04-26 16:04:48.315][function(conn, opt)] Trying to download "https://pubchem.ncbi.nlm.nih.gov/compound/2".
biodb.DEBUG[2025-04-26 16:04:48.542][getUrlContent] Use RCurl for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/compound/2.
biodb.INFO [2025-04-26 16:04:48.699][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.700][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-26 16:04:48.701][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:48.703][biodb::testThat]
biodb.DEBUG[2025-04-26 16:04:48.778][getUrlContent] Use RCurl for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=2&t=l.
biodb.TRACE[2025-04-26 16:04:48.856][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:48.858][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:48.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:48.860][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:48.861][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:48.863][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:48.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:48.865][ef$get] fields variable is a list.
biodb.INFO [2025-04-26 16:04:48.868][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.869][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-04-26 16:04:48.870][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:48.871][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.928][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.929][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-04-26 16:04:48.930][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:48.931][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.949][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.951][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-04-26 16:04:48.952][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:48.953][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.971][biodb::testThat]
biodb.INFO [2025-04-26 16:04:48.973][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-04-26 16:04:48.974][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:48.976][biodb::testThat]
biodb.TRACE[2025-04-26 16:04:48.993][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:04:48.994][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:04:48.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:48.997][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:48.998][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:48.999][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:04:49.000][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.001][ef$get] fields variable is a list.
biodb.INFO [2025-04-26 16:04:49.004][biodb::testThat]
biodb.INFO [2025-04-26 16:04:49.005][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-04-26 16:04:49.006][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:49.007][biodb::testThat]
biodb.INFO [2025-04-26 16:04:49.024][biodb::testThat]
biodb.INFO [2025-04-26 16:04:49.026][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-04-26 16:04:49.027][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:49.028][biodb::testThat]
biodb.INFO [2025-04-26 16:04:49.044][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-26 16:04:49.046][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.pubchem.comp from the request scheduler
biodb.INFO [2025-04-26 16:04:49.047][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2025-04-26 16:04:49.048][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-26 16:04:49.049][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.051][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.053][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.054][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.INFO [2025-04-26 16:04:49.060][biodb::testContext]
biodb.INFO [2025-04-26 16:04:49.061][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:04:49.062][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2025-04-26 16:04:49.063][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:04:49.064][biodb::testContext]
biodb.INFO [2025-04-26 16:04:49.067][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-26 16:04:49.069][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-26 16:04:49.075][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:04:49.076][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-26 16:04:49.077][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-26 16:04:49.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.081][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-26 16:04:49.083][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-26 16:04:49.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.087][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-26 16:04:49.088][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-26 16:04:49.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.092][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-26 16:04:49.094][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-26 16:04:49.095][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-26 16:04:49.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.099][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-26 16:04:49.100][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-26 16:04:49.102][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-26 16:04:49.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.106][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-26 16:04:49.107][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-26 16:04:49.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.111][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-26 16:04:49.112][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-26 16:04:49.114][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-26 16:04:49.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.118][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-26 16:04:49.119][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-26 16:04:49.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.123][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-26 16:04:49.125][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-26 16:04:49.126][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-26 16:04:49.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.130][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:04:49.131][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-26 16:04:49.132][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-26 16:04:49.134][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-26 16:04:49.135][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-26 16:04:49.136][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-26 16:04:49.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.140][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-26 16:04:49.142][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-26 16:04:49.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.146][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-26 16:04:49.147][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-26 16:04:49.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.151][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-26 16:04:49.153][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-26 16:04:49.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.157][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-26 16:04:49.158][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-26 16:04:49.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.162][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-26 16:04:49.164][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-26 16:04:49.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.168][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:04:49.169][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-26 16:04:49.172][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-26 16:04:49.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.177][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-26 16:04:49.178][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-26 16:04:49.179][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-26 16:04:49.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.184][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-26 16:04:49.186][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.187][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-26 16:04:49.188][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.189][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:49.190][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.192][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.193][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.194][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.195][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:04:49.196][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:49.198][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.199][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-26 16:04:49.200][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:49.201][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.202][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.203][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:49.203][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:04:49.203][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:04:49.203][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:04:49.203][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:04:49.205][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:49.206][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.207][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.208][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:49.209][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.210][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.212][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.213][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.214][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:49.215][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:49.216][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.217][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.219][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-26 16:04:49.221][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.222][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:04:49.223][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.224][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:49.225][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.226][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.228][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.229][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.230][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:04:49.231][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:49.232][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.233][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-26 16:04:49.235][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:49.236][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.243][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.244][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:49.244][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:04:49.244][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:04:49.244][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:04:49.244][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:04:49.245][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:49.246][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.247][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.248][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:49.249][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.251][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.252][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.253][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.254][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:49.255][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:49.256][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.257][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.259][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-26 16:04:49.260][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.262][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-26 16:04:49.263][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.264][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:49.265][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.266][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.267][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.269][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.270][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:04:49.271][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:49.272][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.273][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-26 16:04:49.274][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:49.276][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.277][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.278][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.279][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:49.280][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.281][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.282][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:49.283][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.285][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.286][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.287][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.288][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:49.289][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:49.290][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.291][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.293][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-26 16:04:49.295][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.296][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:04:49.297][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.298][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:49.300][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.301][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.302][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.303][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.304][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:04:49.305][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:49.307][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.308][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-26 16:04:49.309][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:49.310][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.311][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.313][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.314][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:04:49.315][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.316][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.317][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:49.318][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.320][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.322][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.323][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:49.324][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:49.325][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.326][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.328][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:04:49.329][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.330][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[2025-04-26 16:04:49.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.341][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[2025-04-26 16:04:49.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.346][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[2025-04-26 16:04:49.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.362][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[2025-04-26 16:04:49.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.378][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[2025-04-26 16:04:49.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.422][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-26 16:04:49.424][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-26 16:04:49.425][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-26 16:04:49.427][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-26 16:04:49.428][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-26 16:04:49.430][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-26 16:04:49.431][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-26 16:04:49.433][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-26 16:04:49.435][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-26 16:04:49.436][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-26 16:04:49.438][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-26 16:04:49.439][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-26 16:04:49.441][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-26 16:04:49.442][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-26 16:04:49.444][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-26 16:04:49.445][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-26 16:04:49.447][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-26 16:04:49.448][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-26 16:04:49.450][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-26 16:04:49.451][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-26 16:04:49.453][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-26 16:04:49.455][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-26 16:04:49.456][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-26 16:04:49.458][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-26 16:04:49.459][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-26 16:04:49.461][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-26 16:04:49.462][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-26 16:04:49.464][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-26 16:04:49.465][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-26 16:04:49.467][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-26 16:04:49.468][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-26 16:04:49.470][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-26 16:04:49.474][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-26 16:04:49.476][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-26 16:04:49.478][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-26 16:04:49.480][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-26 16:04:49.482][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-26 16:04:49.483][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-26 16:04:49.485][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-26 16:04:49.487][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-26 16:04:49.488][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-26 16:04:49.490][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-26 16:04:49.491][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-26 16:04:49.493][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-26 16:04:49.495][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-26 16:04:49.496][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-26 16:04:49.498][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-26 16:04:49.500][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-26 16:04:49.501][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-26 16:04:49.503][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-26 16:04:49.504][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-26 16:04:49.506][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-26 16:04:49.507][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-26 16:04:49.509][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-26 16:04:49.511][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-26 16:04:49.512][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-26 16:04:49.514][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-26 16:04:49.515][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-26 16:04:49.517][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-26 16:04:49.518][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-26 16:04:49.520][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-26 16:04:49.522][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-26 16:04:49.523][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-26 16:04:49.525][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-26 16:04:49.526][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-26 16:04:49.528][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-26 16:04:49.529][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-26 16:04:49.531][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-26 16:04:49.533][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-26 16:04:49.534][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-26 16:04:49.536][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-26 16:04:49.537][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-26 16:04:49.539][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-26 16:04:49.540][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-26 16:04:49.542][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-26 16:04:49.543][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-26 16:04:49.545][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-26 16:04:49.547][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-26 16:04:49.548][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-26 16:04:49.550][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-26 16:04:49.551][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-26 16:04:49.553][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-26 16:04:49.554][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-26 16:04:49.556][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-26 16:04:49.558][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-26 16:04:49.560][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:04:49.561][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.563][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.572][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[2025-04-26 16:04:49.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.593][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[2025-04-26 16:04:49.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.600][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[2025-04-26 16:04:49.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.676][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[2025-04-26 16:04:49.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:04:49.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:04:49.702][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-04-26 16:04:49.704][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-04-26 16:04:49.706][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.708][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-04-26 16:04:49.709][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.710][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:49.711][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.712][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.714][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.715][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.716][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-04-26 16:04:49.717][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:49.718][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.720][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-04-26 16:04:49.721][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:49.722][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-04-26 16:04:49.722][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-04-26 16:04:49.723][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.724][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.725][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-26 16:04:49.727][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.728][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.729][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:49.730][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.731][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.732][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.733][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-04-26 16:04:49.733][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-04-26 16:04:49.735][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:49.736][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:49.737][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.738][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.739][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-04-26 16:04:49.741][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.743][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-04-26 16:04:49.744][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.745][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:49.746][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.747][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.748][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.750][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.751][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-26 16:04:49.752][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:49.753][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.754][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-04-26 16:04:49.756][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:49.757][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-04-26 16:04:49.757][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-04-26 16:04:49.757][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-04-26 16:04:49.757][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-04-26 16:04:49.757][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-04-26 16:04:49.757][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-04-26 16:04:49.758][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.759][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:49.760][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-26 16:04:49.762][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.764][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:49.765][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.766][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.767][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.768][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-04-26 16:04:49.768][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-04-26 16:04:49.770][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:49.771][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:49.772][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.773][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.774][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-04-26 16:04:49.776][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.778][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-04-26 16:04:49.779][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.780][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:49.781][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.782][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.784][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.785][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.786][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-26 16:04:49.787][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:49.788][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.790][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-04-26 16:04:49.791][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:49.792][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-04-26 16:04:49.792][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:49.792][self$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[2025-04-26 16:04:49.792][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:49.792][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:49.792][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:49.792][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:49.792][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:49.792][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:49.792][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:49.792][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-04-26 16:04:49.792][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:49.792][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:49.792][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-04-26 16:04:49.793][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.795][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:04:49.795][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:04:49.795][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:04:49.796][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-04-26 16:04:49.797][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.798][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.799][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:49.800][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.801][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.803][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.804][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-04-26 16:04:49.804][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-04-26 16:04:49.804][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-04-26 16:04:49.805][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:49.806][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:49.807][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.808][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-04-26 16:04:49.810][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-04-26 16:04:49.812][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.813][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-04-26 16:04:49.814][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.815][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:04:49.816][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.818][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.819][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.820][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.821][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-26 16:04:49.822][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:04:49.824][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.825][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-04-26 16:04:49.826][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:04:49.827][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-04-26 16:04:49.827][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-04-26 16:04:49.828][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:04:49.830][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:04:49.831][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-04-26 16:04:49.832][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.833][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.834][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:04:49.835][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:04:49.836][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:04:49.837][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:04:49.839][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-04-26 16:04:49.839][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-04-26 16:04:49.839][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-04-26 16:04:49.840][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:04:49.841][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:04:49.842][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:04:49.843][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-04-26 16:04:49.845][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-04-26 16:04:49.846][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-26 16:04:49.848][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-26 16:04:49.850][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-04-26 16:04:49.852][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-26 16:04:49.853][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-04-26 16:04:49.858][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2025-04-26 16:04:49.860][super$initialize] Register connector ncbi.pubchem.subst with the request scheduler
biodb.DEBUG[2025-04-26 16:04:49.861][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.pubchem.subst.
biodb.DEBUG[2025-04-26 16:04:49.863][private$addConnectorRules] Create new rule for URL "pubchem.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.subst".
biodb.DEBUG[2025-04-26 16:04:49.864][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-04-26 16:04:49.865][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-04-26 16:04:49.867][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.subst".
biodb.DEBUG[2025-04-26 16:04:49.869][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-04-26 16:04:49.870][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-04-26 16:04:49.871][rule$addConnector] Connector "ncbi.pubchem.subst" is already listed in rule "pubchem.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-04-26 16:04:49.877][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2025-04-26 16:04:49.882][biodb::testThat]
biodb.INFO [2025-04-26 16:04:49.884][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-04-26 16:04:49.885][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:49.886][biodb::testThat]
biodb.TRACE[2025-04-26 16:04:49.890][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2025-04-26 16:04:49.892][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:49.895][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-04-26 16:04:49.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:49.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:49.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:49.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:49.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:49.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:49.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:49.913][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:49.914][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:49.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.916][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:49.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:49.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:49.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:49.923][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:49.924][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:49.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.926][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:49.928][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:49.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:49.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:49.933][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:49.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:49.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:49.944][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:49.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:49.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:49.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:49.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:49.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:49.954][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:49.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:49.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:49.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:49.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:49.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:49.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:49.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:49.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:49.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:49.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:49.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:49.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:49.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:49.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:49.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:49.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:49.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:49.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:49.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:49.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:49.987][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2025-04-26 16:04:49.990][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:49.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:49.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:49.995][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-04-26 16:04:49.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-04-26 16:04:49.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:49.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.000][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:50.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-04-26 16:04:50.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.005][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:50.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:50.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.010][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:04:50.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:04:50.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.015][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:50.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:04:50.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.020][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:50.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:04:50.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.048][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:50.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:50.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.089][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:50.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:50.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.094][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:50.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:50.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.102][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:50.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:50.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.146][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.147][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.149][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.165][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:50.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:50.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.170][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:50.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:50.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.174][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:50.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:50.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.179][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:50.180][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:50.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.183][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.184][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:50.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:50.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.198][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.200][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.202][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.209][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:50.210][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-26 16:04:50.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.212][ef$get] fields variable is a list.
biodb.INFO [2025-04-26 16:04:50.225][biodb::testThat]
biodb.INFO [2025-04-26 16:04:50.226][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-26 16:04:50.227][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:50.228][biodb::testThat]
biodb.DEBUG[2025-04-26 16:04:50.231][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-04-26 16:04:50.233][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-26 16:04:50.236][cch$loadFileContent] Trying to load 1 files from cache: [1]: "3".
biodb.TRACE[2025-04-26 16:04:50.238][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-26 16:04:50.240][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75/3.xml".
biodb.DEBUG[2025-04-26 16:04:50.242][conn$getEntryContent] 1 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-04-26 16:04:50.243][self$createEntryFromContent] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:04:50.245][self$createEntryFromContent] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-04-26 16:04:50.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:04:50.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:50.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:50.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:50.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:50.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:50.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:04:50.261][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:50.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:50.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.266][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:50.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-04-26 16:04:50.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:04:50.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:04:50.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:04:50.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:04:50.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:04:50.299][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-04-26 16:04:50.300][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-04-26 16:04:50.315][biodb::testThat]
biodb.INFO [2025-04-26 16:04:50.317][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-26 16:04:50.318][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:50.319][biodb::testThat]
biodb.INFO [2025-04-26 16:04:50.328][biodb::testThat]
biodb.INFO [2025-04-26 16:04:50.329][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-04-26 16:04:50.330][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:50.331][biodb::testThat]
biodb.WARN [2025-04-26 16:04:50.335][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-04-26 16:04:50.339][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-04-26 16:04:50.356][biodb::testThat]
biodb.INFO [2025-04-26 16:04:50.357][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-04-26 16:04:50.358][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:50.360][biodb::testThat]
biodb.INFO [2025-04-26 16:04:50.397][biodb::testThat]
biodb.INFO [2025-04-26 16:04:50.398][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-26 16:04:50.399][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:50.401][biodb::testThat]
biodb.INFO [2025-04-26 16:04:50.411][biodb::testThat]
biodb.INFO [2025-04-26 16:04:50.412][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-26 16:04:50.414][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:50.415][biodb::testThat]
biodb.INFO [2025-04-26 16:04:50.426][biodb::testThat]
biodb.INFO [2025-04-26 16:04:50.427][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-26 16:04:50.428][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:50.429][biodb::testThat]
biodb.DEBUG[2025-04-26 16:04:50.433][function(conn, opt)] Trying to download "https://pubchem.ncbi.nlm.nih.gov/substance/3".
biodb.DEBUG[2025-04-26 16:04:50.504][getUrlContent] Use RCurl for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/substance/3.
biodb.INFO [2025-04-26 16:04:50.644][biodb::testThat]
biodb.INFO [2025-04-26 16:04:50.645][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-26 16:04:50.647][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:04:50.648][biodb::testThat]
biodb.DEBUG[2025-04-26 16:04:50.827][getUrlContent] Use RCurl for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?sid=3&t=l.
biodb.INFO [2025-04-26 16:04:50.906][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-26 16:04:50.907][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.pubchem.subst from the request scheduler
biodb.INFO [2025-04-26 16:04:50.909][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2025-04-26 16:04:50.910][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-26 16:04:50.911][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:04:50.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:04:50.913][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:04:50.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:04:50.915][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:04:50.916][FUN] Functions in observer 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 17 | WARN 1 | SKIP 0 | PASS 672 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_300_pubchem.comp.R:37:1'): RT unit is defined when there is an RT value. ──
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(...)
 4.     └─testthat::quasi_label(enquo(object), label, arg = "object")
 5.       └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by searchable field ──
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by searchable field ──
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
── Failure ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by name. ──
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by name. ──
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
── Failure ('test_long_300_pubchem.comp.R:37:1'): We can load an entry from the database. ──
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
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.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure ('test_long_300_pubchem.comp.R:37:1'): We can load an entry from the database. ──
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")
── Failure ('test_long_300_pubchem.comp.R:37:1'): We can search for a compound ──
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(db = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for a compound ───
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(db = `<NcbPbcCC>`, opt = `<named list>`)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() accepts a single vector. ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): ppm tolerance works in annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): Input data frame is not modified by annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() works correctly with real values. ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): Additional fields are accepted in annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): RT unit is defined when there is an RT value. ──
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(...)
 4.     └─testthat::quasi_label(enquo(object), label, arg = "object")
 5.       └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_long_400_pubchem.subst.R:37:1'): We can load an entry from the database. ──
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure ('test_long_400_pubchem.subst.R:37:1'): We can load an entry from the database. ──
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")

[ FAIL 17 | WARN 1 | SKIP 0 | PASS 672 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck'
* using R version 4.5.0 RC (2025-04-04 r88126 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 '1.12.0'
* 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 whether package 'biodbNcbi' can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.1Mb
  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:
   2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
  ── Failure ('test_long_400_pubchem.subst.R:37:1'): We can load an entry from the database. ──
  `e` inherits from `'NULL'` not `'character'`.
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
   3.   └─testthat::expect_is(e, "BiodbEntry")
  
  [ FAIL 17 | WARN 1 | SKIP 0 | PASS 672 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/00check.log'
for details.

Installation output

biodbNcbi.Rcheck/00install.out

* installing *source* package 'biodbNcbi' ...
** this is package 'biodbNcbi' version '1.12.0'
** 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)