Back to Long Tests report for BioC 3.21

This page was generated on 2025-07-26 23:55 -0400 (Sat, 26 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
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: 2025-07-26 09:55 -0400 (Sat, 26 Jul 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 24.04.2 LTS) / x86_64  ERROR  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

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: 2025-07-26 16:02:43 -0400 (Sat, 26 Jul 2025)
EndedAt: 2025-07-26 16:04:40 -0400 (Sat, 26 Jul 2025)
EllapsedTime: 117.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNcbi.Rcheck
Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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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 [2025-07-26 16:03:34.885][biodb::testContext]
biodb.INFO [2025-07-26 16:03:34.888][biodb::testContext] ********************************************************************************
biodb.INFO [2025-07-26 16:03:34.890][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2025-07-26 16:03:34.891][biodb::testContext] ********************************************************************************
biodb.INFO [2025-07-26 16:03:34.892][biodb::testContext]
biodb.INFO [2025-07-26 16:03:34.898][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-07-26 16:03:34.901][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-07-26 16:03:34.909][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-26 16:03:34.910][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-07-26 16:03:34.911][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-07-26 16:03:34.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:34.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:34.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:34.916][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-07-26 16:03:34.932][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-07-26 16:03:34.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:34.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:34.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:34.936][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-07-26 16:03:34.938][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-07-26 16:03:34.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:34.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:34.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:34.942][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-07-26 16:03:34.943][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-07-26 16:03:34.945][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-07-26 16:03:34.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:34.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:34.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:34.949][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-07-26 16:03:34.950][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-07-26 16:03:34.952][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-07-26 16:03:34.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:34.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:34.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:34.956][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-07-26 16:03:34.957][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-07-26 16:03:34.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:34.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:34.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:34.962][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-07-26 16:03:34.963][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-07-26 16:03:34.964][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-07-26 16:03:34.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:34.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:34.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:34.968][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-07-26 16:03:34.970][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-07-26 16:03:34.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:34.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:34.973][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[2025-07-26 16:03:34.974][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-07-26 16:03:34.975][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-07-26 16:03:34.977][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-07-26 16:03:34.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:34.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:34.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:34.981][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-07-26 16:03:34.982][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-07-26 16:03:34.983][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-07-26 16:03:34.985][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-07-26 16:03:34.986][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-07-26 16:03:34.987][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-07-26 16:03:34.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:34.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:34.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:34.992][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-07-26 16:03:34.993][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-07-26 16:03:34.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:34.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:34.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:34.997][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-07-26 16:03:34.998][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-07-26 16:03:34.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.003][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-07-26 16:03:35.004][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-07-26 16:03:35.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.009][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-07-26 16:03:35.010][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-07-26 16:03:35.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.013][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[2025-07-26 16:03:35.014][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-07-26 16:03:35.015][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-07-26 16:03:35.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.020][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-07-26 16:03:35.021][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-07-26 16:03:35.024][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-07-26 16:03:35.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.027][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[2025-07-26 16:03:35.028][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-07-26 16:03:35.030][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-07-26 16:03:35.031][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-07-26 16:03:35.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.037][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-07-26 16:03:35.065][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.085][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-07-26 16:03:35.087][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.088][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:35.089][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.090][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.092][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.093][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.094][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-07-26 16:03:35.095][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:35.096][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.098][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-07-26 16:03:35.099][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:35.100][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.101][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.103][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:03:35.103][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-26 16:03:35.103][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-26 16:03:35.103][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-07-26 16:03:35.103][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-07-26 16:03:35.104][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:03:35.105][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.106][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.107][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:35.109][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.110][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.111][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.112][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.113][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:35.114][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:35.115][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.117][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.118][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-07-26 16:03:35.120][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.121][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-07-26 16:03:35.123][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.124][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:35.125][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.126][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.127][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.129][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.130][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-07-26 16:03:35.131][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:35.132][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.134][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-07-26 16:03:35.135][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:35.136][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.137][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.138][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:03:35.138][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-26 16:03:35.138][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-26 16:03:35.138][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-07-26 16:03:35.138][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-07-26 16:03:35.140][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:03:35.141][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.142][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.143][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:35.144][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.145][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.147][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.148][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.149][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:35.150][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:35.151][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.153][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.154][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-07-26 16:03:35.156][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.157][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-07-26 16:03:35.158][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.160][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:35.161][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.162][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.163][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.164][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.166][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-07-26 16:03:35.167][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:35.168][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.169][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-07-26 16:03:35.170][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:35.172][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.173][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.174][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.175][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:03:35.176][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.178][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.179][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:35.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.182][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.183][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.185][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:35.186][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:35.187][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.188][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.189][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-07-26 16:03:35.191][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.193][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-07-26 16:03:35.194][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.195][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:35.196][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.197][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.199][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.200][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.201][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-07-26 16:03:35.202][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:35.204][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.205][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-07-26 16:03:35.206][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:35.207][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.208][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.210][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.211][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:03:35.212][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.213][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.214][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:35.215][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.217][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.218][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.219][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.220][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:35.221][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:35.222][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.224][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.227][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-26 16:03:35.228][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.240][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[2025-07-26 16:03:35.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.268][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[2025-07-26 16:03:35.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.328][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[2025-07-26 16:03:35.329][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-07-26 16:03:35.333][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-07-26 16:03:35.335][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-07-26 16:03:35.337][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-07-26 16:03:35.338][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-07-26 16:03:35.340][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-07-26 16:03:35.341][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-07-26 16:03:35.343][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-07-26 16:03:35.344][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-07-26 16:03:35.346][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-07-26 16:03:35.348][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-07-26 16:03:35.349][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-07-26 16:03:35.351][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-07-26 16:03:35.352][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-07-26 16:03:35.354][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-07-26 16:03:35.355][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-07-26 16:03:35.357][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-07-26 16:03:35.359][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-07-26 16:03:35.360][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-07-26 16:03:35.362][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-07-26 16:03:35.363][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-07-26 16:03:35.365][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-07-26 16:03:35.367][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-07-26 16:03:35.368][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-07-26 16:03:35.370][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-07-26 16:03:35.371][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-07-26 16:03:35.373][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-07-26 16:03:35.374][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-07-26 16:03:35.376][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-07-26 16:03:35.378][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-07-26 16:03:35.379][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-07-26 16:03:35.381][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-07-26 16:03:35.382][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-07-26 16:03:35.384][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-07-26 16:03:35.385][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-07-26 16:03:35.387][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-07-26 16:03:35.388][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-07-26 16:03:35.390][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-07-26 16:03:35.392][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-07-26 16:03:35.393][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-07-26 16:03:35.395][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-07-26 16:03:35.396][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-07-26 16:03:35.398][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-07-26 16:03:35.400][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-07-26 16:03:35.401][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-07-26 16:03:35.403][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-07-26 16:03:35.404][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-07-26 16:03:35.406][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-07-26 16:03:35.407][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-07-26 16:03:35.409][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-07-26 16:03:35.411][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-07-26 16:03:35.412][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-07-26 16:03:35.414][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-07-26 16:03:35.415][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-07-26 16:03:35.417][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-07-26 16:03:35.418][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-07-26 16:03:35.420][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-07-26 16:03:35.422][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-07-26 16:03:35.423][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-07-26 16:03:35.425][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-07-26 16:03:35.426][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-07-26 16:03:35.428][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-07-26 16:03:35.429][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-07-26 16:03:35.431][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-07-26 16:03:35.433][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-07-26 16:03:35.434][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-07-26 16:03:35.436][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-07-26 16:03:35.437][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-07-26 16:03:35.439][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-07-26 16:03:35.440][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-07-26 16:03:35.442][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-07-26 16:03:35.443][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-07-26 16:03:35.445][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-07-26 16:03:35.447][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-07-26 16:03:35.448][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-07-26 16:03:35.450][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-07-26 16:03:35.451][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-07-26 16:03:35.453][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-07-26 16:03:35.454][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-07-26 16:03:35.456][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-07-26 16:03:35.457][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-07-26 16:03:35.459][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-07-26 16:03:35.461][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-07-26 16:03:35.483][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-07-26 16:03:35.486][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-07-26 16:03:35.489][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-26 16:03:35.490][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.492][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.539][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[2025-07-26 16:03:35.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.564][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[2025-07-26 16:03:35.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:35.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:35.661][bdb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-07-26 16:03:35.670][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-07-26 16:03:35.672][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.674][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-07-26 16:03:35.675][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.676][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:35.677][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.678][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.680][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.681][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.682][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-07-26 16:03:35.683][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:35.684][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.686][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-07-26 16:03:35.687][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:35.688][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-07-26 16:03:35.688][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-07-26 16:03:35.689][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.690][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.692][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-07-26 16:03:35.693][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.694][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.695][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:35.696][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.697][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.698][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.700][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-07-26 16:03:35.700][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-07-26 16:03:35.701][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:35.702][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:35.703][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.704][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.706][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-07-26 16:03:35.708][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.709][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-07-26 16:03:35.710][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.711][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:35.712][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.714][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.715][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.716][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.717][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-07-26 16:03:35.718][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:35.719][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.721][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-07-26 16:03:35.722][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:35.723][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-07-26 16:03:35.723][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-07-26 16:03:35.723][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-07-26 16:03:35.723][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-07-26 16:03:35.723][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-07-26 16:03:35.723][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-07-26 16:03:35.724][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.726][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:03:35.727][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-07-26 16:03:35.728][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.729][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.730][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:35.731][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.732][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.733][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.735][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-07-26 16:03:35.735][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-07-26 16:03:35.736][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:35.737][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:35.738][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.739][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.741][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-07-26 16:03:35.743][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.744][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-07-26 16:03:35.750][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.751][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:35.752][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.754][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.755][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.756][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.757][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-07-26 16:03:35.758][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:35.759][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.761][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-07-26 16:03:35.762][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:35.763][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-07-26 16:03:35.763][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:35.763][self$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[2025-07-26 16:03:35.763][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:35.763][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:35.763][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:35.763][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:35.763][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:35.763][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:35.763][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:35.763][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-07-26 16:03:35.763][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:35.763][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:35.763][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:35.764][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.766][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:03:35.766][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-26 16:03:35.766][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-26 16:03:35.767][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-07-26 16:03:35.768][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.770][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:35.771][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.772][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.773][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.775][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-07-26 16:03:35.775][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-07-26 16:03:35.775][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-07-26 16:03:35.776][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:35.777][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:35.778][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.779][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-07-26 16:03:35.781][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-07-26 16:03:35.783][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.784][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-07-26 16:03:35.785][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.786][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:35.788][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.789][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.790][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.791][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.792][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-07-26 16:03:35.794][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:35.795][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.796][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-07-26 16:03:35.797][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:35.798][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-07-26 16:03:35.798][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-07-26 16:03:35.800][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:35.801][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:35.802][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-07-26 16:03:35.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.805][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:35.807][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:35.808][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:35.809][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:35.810][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-07-26 16:03:35.810][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-07-26 16:03:35.810][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-07-26 16:03:35.811][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:35.812][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:35.813][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:35.815][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-07-26 16:03:35.820][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-07-26 16:03:35.822][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-07-26 16:03:35.824][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-07-26 16:03:35.825][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-07-26 16:03:35.827][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-07-26 16:03:35.829][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-07-26 16:03:35.848][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-07-26 16:03:35.850][initialize] Register connector ncbi.ccds with the request scheduler
biodb.DEBUG[2025-07-26 16:03:35.853][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.ccds.
biodb.DEBUG[2025-07-26 16:03:35.857][private$addConnectorRules] Create new rule for URL "www.ncbi.nlm.nih.gov" of connector "ncbi.ccds".
biodb.DEBUG[2025-07-26 16:03:35.861][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-07-26 16:03:35.862][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-07-26 16:03:35.864][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.ccds".
biodb.DEBUG[2025-07-26 16:03:35.865][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-07-26 16:03:35.866][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-07-26 16:03:35.868][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2025-07-26 16:03:35.877][biodb::testThat]
biodb.INFO [2025-07-26 16:03:35.878][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-07-26 16:03:35.879][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:03:35.881][biodb::testThat]
biodb.TRACE[2025-07-26 16:03:35.887][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2025-07-26 16:03:35.889][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:03:35.892][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-07-26 16:03:35.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:35.900][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:35.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:35.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:35.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:35.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:35.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:03:35.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:35.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:35.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:35.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:35.952][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:35.963][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:35.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:35.976][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:35.999][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:36.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.005][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.010][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.020][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:36.081][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2025-07-26 16:03:36.085][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.089][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.118][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:03:36.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:03:36.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.123][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:03:36.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:03:36.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.128][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:03:36.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:03:36.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.133][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:03:36.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:03:36.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.176][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.218][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.223][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.228][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.257][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.258][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.260][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.277][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:36.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.287][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.292][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.297][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:36.298][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.300][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.301][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:36.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.316][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.317][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.320][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.327][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.328][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.330][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.349][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2025-07-26 16:03:36.380][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:03:36.381][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-07-26 16:03:36.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:36.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:36.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:36.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:36.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:36.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:36.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:03:36.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.431][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:36.433][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.435][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.437][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:36.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.442][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.446][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.456][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:36.490][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2025-07-26 16:03:36.508][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.513][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.518][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:03:36.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:03:36.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.523][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:03:36.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:03:36.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.528][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:03:36.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:03:36.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.533][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:03:36.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:03:36.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.549][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.595][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.599][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.604][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:36.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.644][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.646][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.649][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.667][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:36.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.672][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.677][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.681][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:36.683][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.685][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.686][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:36.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.701][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.703][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:36.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.705][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:36.712][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:36.713][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:36.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:36.715][ef$get] fields variable is a list.
biodb.INFO [2025-07-26 16:03:36.727][biodb::testThat]
biodb.INFO [2025-07-26 16:03:36.729][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-07-26 16:03:36.730][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:03:36.731][biodb::testThat]
biodb.DEBUG[2025-07-26 16:03:36.734][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2025-07-26 16:03:36.740][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
biodb.TRACE[2025-07-26 16:03:36.746][cch$loadFileContent] Trying to load 2 files from cache: [2]: "CCDS12227.1, CCDS43240.1".
biodb.INFO [2025-07-26 16:03:36.747][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704" for "ncbi.ccds-c3bf0257a03be04fd46e362b99907704".
biodb.TRACE[2025-07-26 16:03:36.750][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2025-07-26 16:03:36.751][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-07-26 16:03:36.752][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-07-26 16:03:36.753][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-07-26 16:03:36.755][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-07-26 16:03:36.756][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-07-26 16:03:36.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:36.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:36.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:36.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:36.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:36.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:36.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:36.782][scheduler$sendRequest] Getting content of get URL request "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.DEBUG[2025-07-26 16:03:36.800][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:36.801][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:36.802][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-07-26 16:03:37.253][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-07-26 16:03:37.342][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:37.343][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:37.344][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:37.358][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-07-26 16:03:37.484][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-07-26 16:03:37.550][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:37.551][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:37.552][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:37.554][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-07-26 16:03:37.700][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-07-26 16:03:37.774][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:37.775][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:37.777][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:37.778][rule$waitAsNeeded] Wait 0.0241129 second(s).
biodb.TRACE[2025-07-26 16:03:37.810][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-07-26 16:03:37.943][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-07-26 16:03:38.020][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:38.022][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:38.023][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:38.024][rule$waitAsNeeded] Wait 0.333143 second(s).
biodb.TRACE[2025-07-26 16:03:38.374][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-07-26 16:03:38.504][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-07-26 16:03:38.581][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:38.583][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:38.584][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:38.586][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-07-26 16:03:38.721][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-07-26 16:03:38.792][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:38.794][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:38.795][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:38.797][rule$waitAsNeeded] Wait 0.012675 second(s).
biodb.TRACE[2025-07-26 16:03:38.811][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-07-26 16:03:38.937][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-07-26 16:03:39.006][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:39.007][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:39.009][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:39.010][rule$waitAsNeeded] Wait 0.363235 second(s).
biodb.TRACE[2025-07-26 16:03:39.376][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-07-26 16:03:39.521][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-07-26 16:03:39.586][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:39.587][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:39.588][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:39.590][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-07-26 16:03:39.724][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-07-26 16:03:39.807][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:39.809][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:39.810][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:39.811][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-07-26 16:03:39.942][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-07-26 16:03:40.013][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:40.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:40.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:40.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:40.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:40.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:40.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:40.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:40.060][scheduler$sendRequest] Getting content of get URL request "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.DEBUG[2025-07-26 16:03:40.075][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:40.076][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:40.078][rule$waitAsNeeded] Wait 0.297334 second(s).
biodb.TRACE[2025-07-26 16:03:40.380][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-07-26 16:03:40.518][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-07-26 16:03:40.589][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:40.590][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:40.591][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:40.593][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-07-26 16:03:40.735][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-07-26 16:03:40.803][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:40.805][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:40.806][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:40.807][rule$waitAsNeeded] Wait 0.00417304 second(s).
biodb.TRACE[2025-07-26 16:03:40.815][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-07-26 16:03:40.941][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-07-26 16:03:41.012][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:41.013][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:41.014][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:41.016][rule$waitAsNeeded] Wait 0.360775 second(s).
biodb.TRACE[2025-07-26 16:03:41.379][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-07-26 16:03:41.507][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-07-26 16:03:41.577][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:41.579][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:41.580][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:41.581][rule$waitAsNeeded] Wait 0.011539 second(s).
biodb.TRACE[2025-07-26 16:03:41.598][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-07-26 16:03:41.725][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-07-26 16:03:41.790][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:41.791][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:41.793][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:41.794][rule$waitAsNeeded] Wait 0.0207899 second(s).
biodb.TRACE[2025-07-26 16:03:41.817][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-07-26 16:03:41.943][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-07-26 16:03:42.020][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:42.022][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:42.023][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:42.024][rule$waitAsNeeded] Wait 0.354199 second(s).
biodb.TRACE[2025-07-26 16:03:42.381][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-07-26 16:03:42.508][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-07-26 16:03:42.580][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:42.582][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:42.583][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:42.584][rule$waitAsNeeded] Wait 0.0130689 second(s).
biodb.TRACE[2025-07-26 16:03:42.600][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-07-26 16:03:42.724][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-07-26 16:03:42.800][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:42.801][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:42.802][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:42.804][rule$waitAsNeeded] Wait 0.0127201 second(s).
biodb.TRACE[2025-07-26 16:03:42.819][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-07-26 16:03:42.942][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-07-26 16:03:43.016][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:43.017][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:43.018][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:43.020][rule$waitAsNeeded] Wait 0.360806 second(s).
biodb.TRACE[2025-07-26 16:03:43.383][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-07-26 16:03:43.508][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-07-26 16:03:43.572][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.TRACE[2025-07-26 16:03:43.575][private$doSaveContentToFile] Saving to 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[2025-07-26 16:03:43.578][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-07-26 16:03:43.579][self$createEntryFromContent] Creating NCBI CCDS entries from 2 content(s).
biodb.DEBUG[2025-07-26 16:03:43.581][self$createEntryFromContent] Parsing 2 NCBI CCDS entries.
biodb.DEBUG[2025-07-26 16:03:43.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:43.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:43.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:43.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:43.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:43.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:43.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:03:43.597][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:43.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:43.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:43.602][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:43.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:43.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:43.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:43.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:43.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:43.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:43.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:43.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:43.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:43.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:43.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:43.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:03:43.627][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:43.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:43.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:43.632][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:43.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:43.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:43.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:43.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:43.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:43.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:43.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:43.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:43.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:43.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:43.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:43.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:43.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:43.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:43.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:43.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:43.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:43.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:43.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:43.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:43.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:43.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:43.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:43.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:43.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:43.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:43.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:43.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:43.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:43.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:43.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:43.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:43.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:43.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:43.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:43.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:43.700][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2025-07-26 16:03:43.701][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-07-26 16:03:43.719][biodb::testThat]
biodb.INFO [2025-07-26 16:03:43.721][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-07-26 16:03:43.722][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:03:43.723][biodb::testThat]
biodb.INFO [2025-07-26 16:03:43.732][biodb::testThat]
biodb.INFO [2025-07-26 16:03:43.734][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-07-26 16:03:43.735][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:03:43.736][biodb::testThat]
biodb.WARN [2025-07-26 16:03:43.754][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-07-26 16:03:43.771][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-07-26 16:03:43.784][biodb::testThat]
biodb.INFO [2025-07-26 16:03:43.786][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-07-26 16:03:43.787][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:03:43.788][biodb::testThat]
biodb.INFO [2025-07-26 16:03:44.039][biodb::testThat]
biodb.INFO [2025-07-26 16:03:44.040][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-07-26 16:03:44.042][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:03:44.043][biodb::testThat]
biodb.INFO [2025-07-26 16:03:44.055][biodb::testThat]
biodb.INFO [2025-07-26 16:03:44.056][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-07-26 16:03:44.057][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:03:44.058][biodb::testThat]
biodb.INFO [2025-07-26 16:03:44.069][biodb::testThat]
biodb.INFO [2025-07-26 16:03:44.070][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-07-26 16:03:44.071][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:03:44.073][biodb::testThat]
biodb.DEBUG[2025-07-26 16:03:44.077][function(conn, opt)] Trying to download "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.DEBUG[2025-07-26 16:03:44.198][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 [2025-07-26 16:03:44.326][biodb::testThat]
biodb.INFO [2025-07-26 16:03:44.328][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-07-26 16:03:44.329][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:03:44.330][biodb::testThat]
biodb.INFO [2025-07-26 16:03:44.339][bdb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-07-26 16:03:44.340][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.ccds from the request scheduler
biodb.INFO [2025-07-26 16:03:44.342][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-07-26 16:03:44.343][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-07-26 16:03:44.344][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:44.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:44.346][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.348][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-07-26 16:03:44.360][biodb::testContext]
biodb.INFO [2025-07-26 16:03:44.362][biodb::testContext] ********************************************************************************
biodb.INFO [2025-07-26 16:03:44.363][biodb::testContext] Test context - Gene long tests
biodb.INFO [2025-07-26 16:03:44.364][biodb::testContext] ********************************************************************************
biodb.INFO [2025-07-26 16:03:44.365][biodb::testContext]
biodb.INFO [2025-07-26 16:03:44.368][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-07-26 16:03:44.370][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-07-26 16:03:44.376][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-26 16:03:44.377][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-07-26 16:03:44.378][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-07-26 16:03:44.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.383][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-07-26 16:03:44.552][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-07-26 16:03:44.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.557][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-07-26 16:03:44.558][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-07-26 16:03:44.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.563][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-07-26 16:03:44.564][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-07-26 16:03:44.565][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-07-26 16:03:44.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.569][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-07-26 16:03:44.570][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-07-26 16:03:44.572][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-07-26 16:03:44.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.576][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-07-26 16:03:44.577][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-07-26 16:03:44.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.581][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-07-26 16:03:44.583][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-07-26 16:03:44.584][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-07-26 16:03:44.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.588][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-07-26 16:03:44.589][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-07-26 16:03:44.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.594][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-07-26 16:03:44.595][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-07-26 16:03:44.596][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-07-26 16:03:44.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.600][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-07-26 16:03:44.602][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-07-26 16:03:44.603][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-07-26 16:03:44.604][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-07-26 16:03:44.605][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-07-26 16:03:44.606][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-07-26 16:03:44.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.611][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-07-26 16:03:44.612][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-07-26 16:03:44.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.615][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[2025-07-26 16:03:44.616][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-07-26 16:03:44.618][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-07-26 16:03:44.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.622][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-07-26 16:03:44.623][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-07-26 16:03:44.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.628][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-07-26 16:03:44.629][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-07-26 16:03:44.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.634][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-07-26 16:03:44.635][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-07-26 16:03:44.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.640][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-07-26 16:03:44.641][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-07-26 16:03:44.644][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-07-26 16:03:44.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.649][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-07-26 16:03:44.650][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-07-26 16:03:44.651][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-07-26 16:03:44.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.656][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-07-26 16:03:44.658][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:44.659][self$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[2025-07-26 16:03:44.660][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.662][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:44.663][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.664][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:44.665][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:44.667][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:44.668][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-07-26 16:03:44.669][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:44.670][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.672][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-07-26 16:03:44.673][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:44.674][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:44.675][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.677][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:03:44.677][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-26 16:03:44.677][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-26 16:03:44.677][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-07-26 16:03:44.677][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-07-26 16:03:44.678][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:03:44.679][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:44.680][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:44.682][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:44.683][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:44.684][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:44.685][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:44.687][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:44.688][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:44.689][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:44.690][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:44.692][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:44.693][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-07-26 16:03:44.695][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:44.697][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-07-26 16:03:44.698][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.700][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:44.701][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.702][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:44.703][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:44.705][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:44.706][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-07-26 16:03:44.707][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:44.709][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.710][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-07-26 16:03:44.711][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:44.713][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:44.714][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.715][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:03:44.715][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-26 16:03:44.715][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-26 16:03:44.715][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-07-26 16:03:44.715][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-07-26 16:03:44.717][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:03:44.718][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:44.719][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:44.721][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:44.722][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:44.723][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:44.724][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:44.726][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:44.727][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:44.728][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:44.729][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:44.731][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:44.732][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-07-26 16:03:44.734][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.736][self$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[2025-07-26 16:03:44.737][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.738][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:44.740][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.741][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:44.742][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:44.744][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:44.745][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-07-26 16:03:44.746][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:44.748][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:44.749][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-07-26 16:03:44.751][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:44.752][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:44.753][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.755][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:44.756][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:03:44.757][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:44.759][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:44.760][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:44.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:44.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:44.764][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:44.765][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:44.766][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:44.767][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:44.769][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:44.770][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:44.771][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-07-26 16:03:44.774][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.775][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-07-26 16:03:44.776][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.778][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:44.779][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.780][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:44.782][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:44.783][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:44.784][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-07-26 16:03:44.785][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:44.787][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:44.788][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-07-26 16:03:44.789][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:44.791][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:44.792][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:44.794][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:44.795][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:03:44.796][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:44.798][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:44.799][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:44.800][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:44.802][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:44.803][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:44.804][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:44.806][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:44.807][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:44.808][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:44.809][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:44.811][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-26 16:03:44.812][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.844][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[2025-07-26 16:03:44.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.850][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[2025-07-26 16:03:44.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.856][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[2025-07-26 16:03:44.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.862][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[2025-07-26 16:03:44.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.874][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.DEBUG[2025-07-26 16:03:44.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:44.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:44.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:44.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:44.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:44.918][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-07-26 16:03:44.920][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-07-26 16:03:44.922][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-07-26 16:03:44.924][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-07-26 16:03:44.926][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-07-26 16:03:44.927][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-07-26 16:03:44.929][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-07-26 16:03:44.931][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-07-26 16:03:44.933][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-07-26 16:03:44.934][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-07-26 16:03:44.936][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-07-26 16:03:44.938][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-07-26 16:03:44.940][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-07-26 16:03:44.941][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-07-26 16:03:44.943][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-07-26 16:03:44.945][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-07-26 16:03:44.947][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-07-26 16:03:44.948][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-07-26 16:03:44.950][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-07-26 16:03:44.952][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-07-26 16:03:44.954][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-07-26 16:03:44.955][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-07-26 16:03:44.957][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-07-26 16:03:44.959][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-07-26 16:03:44.961][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-07-26 16:03:44.962][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-07-26 16:03:44.964][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-07-26 16:03:44.966][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-07-26 16:03:44.967][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-07-26 16:03:44.969][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-07-26 16:03:44.971][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-07-26 16:03:44.973][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-07-26 16:03:44.974][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-07-26 16:03:44.976][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-07-26 16:03:44.978][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-07-26 16:03:44.980][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-07-26 16:03:44.982][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-07-26 16:03:44.983][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-07-26 16:03:44.985][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-07-26 16:03:44.987][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-07-26 16:03:44.988][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-07-26 16:03:44.990][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-07-26 16:03:44.992][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-07-26 16:03:44.994][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-07-26 16:03:44.996][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-07-26 16:03:44.997][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-07-26 16:03:44.999][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-07-26 16:03:45.001][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-07-26 16:03:45.003][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-07-26 16:03:45.004][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-07-26 16:03:45.006][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-07-26 16:03:45.008][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-07-26 16:03:45.010][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-07-26 16:03:45.011][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-07-26 16:03:45.013][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-07-26 16:03:45.015][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-07-26 16:03:45.017][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-07-26 16:03:45.019][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-07-26 16:03:45.020][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-07-26 16:03:45.022][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-07-26 16:03:45.024][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-07-26 16:03:45.025][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-07-26 16:03:45.027][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-07-26 16:03:45.029][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-07-26 16:03:45.031][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-07-26 16:03:45.032][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-07-26 16:03:45.034][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-07-26 16:03:45.036][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-07-26 16:03:45.038][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-07-26 16:03:45.039][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-07-26 16:03:45.041][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-07-26 16:03:45.043][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-07-26 16:03:45.045][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-07-26 16:03:45.046][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-07-26 16:03:45.048][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-07-26 16:03:45.050][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-07-26 16:03:45.057][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-07-26 16:03:45.058][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-07-26 16:03:45.060][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-07-26 16:03:45.061][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-07-26 16:03:45.063][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-07-26 16:03:45.065][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-07-26 16:03:45.066][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-07-26 16:03:45.068][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-07-26 16:03:45.070][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-07-26 16:03:45.071][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-26 16:03:45.072][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.074][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:45.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.083][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[2025-07-26 16:03:45.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:45.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:45.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.105][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[2025-07-26 16:03:45.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:45.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:45.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:45.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.135][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[2025-07-26 16:03:45.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:45.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.150][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[2025-07-26 16:03:45.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:45.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:45.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:45.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:45.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:45.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.195][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[2025-07-26 16:03:45.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:03:45.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.202][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[2025-07-26 16:03:45.206][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-07-26 16:03:45.208][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-07-26 16:03:45.210][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.211][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-07-26 16:03:45.212][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.214][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:45.215][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.216][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:45.217][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.218][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:45.220][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-07-26 16:03:45.221][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:45.222][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.223][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-07-26 16:03:45.224][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:45.225][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-07-26 16:03:45.225][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-07-26 16:03:45.227][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:45.228][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:45.229][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-07-26 16:03:45.230][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:45.231][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:45.232][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:45.234][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:45.235][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:45.236][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:45.237][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-07-26 16:03:45.237][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-07-26 16:03:45.238][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:45.239][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:45.240][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.241][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:45.243][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-07-26 16:03:45.245][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.246][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-07-26 16:03:45.249][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.250][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:45.251][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.252][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:45.253][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.255][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:45.256][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-07-26 16:03:45.257][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:45.258][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.259][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-07-26 16:03:45.261][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:45.262][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-07-26 16:03:45.262][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-07-26 16:03:45.262][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-07-26 16:03:45.262][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-07-26 16:03:45.262][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-07-26 16:03:45.262][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-07-26 16:03:45.263][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:45.264][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:03:45.265][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-07-26 16:03:45.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:45.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:45.269][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:45.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:45.271][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:45.272][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:45.273][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-07-26 16:03:45.273][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-07-26 16:03:45.274][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:45.276][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:45.277][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.278][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:45.279][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-07-26 16:03:45.281][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:45.282][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-07-26 16:03:45.284][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.285][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:45.286][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.287][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:45.288][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.290][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:45.291][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-07-26 16:03:45.292][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:45.293][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.294][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-07-26 16:03:45.295][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:45.297][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-07-26 16:03:45.297][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:45.297][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:45.297][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:45.297][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:45.297][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:45.297][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:45.297][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:45.297][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:45.297][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:45.297][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-07-26 16:03:45.297][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:45.297][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:45.297][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:03:45.298][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:45.299][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:03:45.299][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-26 16:03:45.299][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-26 16:03:45.300][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-07-26 16:03:45.302][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:45.303][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:45.304][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:45.305][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:45.306][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:45.307][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:45.308][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-07-26 16:03:45.308][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-07-26 16:03:45.308][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-07-26 16:03:45.310][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:45.311][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:45.312][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.313][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-07-26 16:03:45.314][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-07-26 16:03:45.316][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.318][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-07-26 16:03:45.319][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.320][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:03:45.321][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.322][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:03:45.323][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.325][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:03:45.326][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-07-26 16:03:45.327][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:03:45.328][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.329][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-07-26 16:03:45.330][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:03:45.332][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-07-26 16:03:45.332][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-07-26 16:03:45.333][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:03:45.334][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:03:45.335][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-07-26 16:03:45.336][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:45.337][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:45.339][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:03:45.340][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:03:45.341][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:03:45.342][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:03:45.343][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-07-26 16:03:45.343][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-07-26 16:03:45.343][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-07-26 16:03:45.344][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:03:45.345][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:03:45.347][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:03:45.348][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-07-26 16:03:45.349][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-07-26 16:03:45.351][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-07-26 16:03:45.353][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-07-26 16:03:45.354][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-07-26 16:03:45.356][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-07-26 16:03:45.358][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-07-26 16:03:45.365][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2025-07-26 16:03:45.366][super$initialize] Register connector ncbi.gene with the request scheduler
biodb.DEBUG[2025-07-26 16:03:45.368][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.gene.
biodb.DEBUG[2025-07-26 16:03:45.369][private$addConnectorRules] Create new rule for URL "www.ncbi.nlm.nih.gov" of connector "ncbi.gene".
biodb.DEBUG[2025-07-26 16:03:45.371][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-07-26 16:03:45.372][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-07-26 16:03:45.374][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.gene".
biodb.DEBUG[2025-07-26 16:03:45.375][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-07-26 16:03:45.376][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-07-26 16:03:45.434][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2025-07-26 16:03:45.440][biodb::testThat]
biodb.INFO [2025-07-26 16:03:45.441][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-07-26 16:03:45.442][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:03:45.443][biodb::testThat]
biodb.TRACE[2025-07-26 16:03:45.457][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[2025-07-26 16:03:45.458][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:03:45.462][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-07-26 16:03:45.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:45.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.476][FUN] Functions in observer BiodbConfig: [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[2025-07-26 16:03:45.489][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:45.491][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:45.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.493][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:45.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:45.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.500][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:45.501][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:45.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.504][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.506][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:45.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:45.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.511][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:45.512][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:45.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.514][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.517][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:45.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:45.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.522][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:45.523][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:45.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.525][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.527][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:45.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:45.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.540][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:45.541][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:45.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.543][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.546][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:45.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:45.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.551][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:45.552][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:45.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.554][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.557][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:45.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:45.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.566][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:45.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:45.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.571][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:45.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:45.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.575][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:45.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:45.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:45.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:45.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.585][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:45.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:45.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:45.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:45.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:45.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:45.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:45.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:45.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:45.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:45.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:45.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:45.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:45.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:45.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:45.618][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2025-07-26 16:03:45.621][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:45.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:45.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.626][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:45.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:45.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.631][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:45.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:45.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.635][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:45.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:45.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:45.643][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:45.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:45.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:45.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:45.648][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-07-26 16:03:45.673][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-07-26 16:03:45.675][initialize] Register connector ncbi.ccds with the request scheduler
biodb.DEBUG[2025-07-26 16:03:45.676][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.ccds.
biodb.DEBUG[2025-07-26 16:03:45.691][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2025-07-26 16:03:45.692][self$recomputeFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-07-26 16:03:45.694][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2025-07-26 16:03:45.705][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-07-26 16:03:45.706][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-07-26 16:03:45.708][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2025-07-26 16:03:45.709][self$recomputeFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-07-26 16:03:45.710][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2025-07-26 16:03:45.711][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-07-26 16:03:45.712][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-07-26 16:03:45.724][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2025-07-26 16:03:45.725][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2025-07-26 16:03:45.727][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-07-26 16:03:45.731][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS14416.1".
biodb.TRACE[2025-07-26 16:03:45.732][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-07-26 16:03:45.734][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-07-26 16:03:45.735][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-07-26 16:03:45.736][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-07-26 16:03:45.737][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-07-26 16:03:45.739][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-07-26 16:03:45.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:45.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:45.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:45.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:45.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:45.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:45.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:45.756][scheduler$sendRequest] Getting content of get URL request "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.DEBUG[2025-07-26 16:03:45.759][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:45.760][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:45.761][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-07-26 16:03:45.907][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-07-26 16:03:45.970][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:45.971][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:45.973][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:45.974][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-07-26 16:03:46.111][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-07-26 16:03:46.192][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:46.193][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:46.195][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:46.196][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-07-26 16:03:46.318][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-07-26 16:03:46.383][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:46.384][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:46.385][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:46.387][rule$waitAsNeeded] Wait 0.374498 second(s).
biodb.TRACE[2025-07-26 16:03:46.765][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-07-26 16:03:46.891][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-07-26 16:03:46.958][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:46.959][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:46.960][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:46.962][rule$waitAsNeeded] Wait 0.0121799 second(s).
biodb.TRACE[2025-07-26 16:03:46.984][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-07-26 16:03:47.114][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-07-26 16:03:47.194][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:47.196][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:47.197][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:47.199][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-07-26 16:03:47.335][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-07-26 16:03:47.417][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:47.418][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:47.420][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:47.421][rule$waitAsNeeded] Wait 0.343553 second(s).
biodb.TRACE[2025-07-26 16:03:47.767][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-07-26 16:03:47.895][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-07-26 16:03:47.960][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:47.962][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:47.963][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:47.965][rule$waitAsNeeded] Wait 0.019196 second(s).
biodb.TRACE[2025-07-26 16:03:47.986][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-07-26 16:03:48.113][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-07-26 16:03:48.183][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:48.185][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:48.186][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:48.187][rule$waitAsNeeded] Wait 0.0110672 second(s).
biodb.TRACE[2025-07-26 16:03:48.206][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-07-26 16:03:48.334][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-07-26 16:03:48.404][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:48.405][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:48.406][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:48.408][rule$waitAsNeeded] Wait 0.359047 second(s).
biodb.TRACE[2025-07-26 16:03:48.769][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-07-26 16:03:48.897][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-07-26 16:03:48.963][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1". Retrying connection to server...
biodb.TRACE[2025-07-26 16:03:48.966][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS14416.1.html"
biodb.DEBUG[2025-07-26 16:03:48.968][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-07-26 16:03:48.970][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:03:48.971][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-07-26 16:03:48.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:48.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:48.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:48.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:48.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:48.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:48.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:03:48.988][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:48.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:48.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:48.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:48.993][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:48.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:48.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:48.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:48.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:48.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:49.027][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-07-26 16:03:49.028][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.TRACE[2025-07-26 16:03:49.029][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:03:49.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:03:49.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.034][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:03:49.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:03:49.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.039][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:03:49.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:03:49.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.044][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:03:49.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:03:49.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.060][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:49.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:49.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.116][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:49.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:49.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.121][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:49.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:49.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.125][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:49.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:49.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.153][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.154][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.156][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.172][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:49.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:49.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.177][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:49.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:49.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.182][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:49.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:49.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.187][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:49.188][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:49.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.191][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.192][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:49.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:49.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.207][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:49.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:49.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.212][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:49.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:49.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.217][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:49.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:49.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.221][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:49.223][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:49.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.225][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.226][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:49.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:49.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.241][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.246][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.251][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.256][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.257][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.260][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.261][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.275][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.280][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.285][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.290][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.291][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.294][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.295][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.309][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:49.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:49.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.314][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:49.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:49.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.319][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:49.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:49.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.324][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:49.325][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:49.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.328][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.329][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:49.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:49.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.344][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:49.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:49.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:03:49.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:49.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.354][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:03:49.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:49.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.359][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:49.360][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:49.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.362][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.364][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:49.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:49.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.378][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:49.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:49.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.383][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:49.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:49.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.395][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:49.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:49.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.400][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:49.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:49.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.405][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.409][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.414][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:49.419][private$computeField] Compute value for field "aa.seq".
biodb.TRACE[2025-07-26 16:03:49.420][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:49.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:49.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.425][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:49.427][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:49.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.429][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.430][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:49.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:49.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.466][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:49.468][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:49.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.470][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.477][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.478][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.480][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.487][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:49.488][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:49.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.491][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.497][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:49.499][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:49.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.501][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.508][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:03:49.509][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:49.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.512][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.518][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.520][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.522][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.529][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.531][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.533][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.561][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-3002-content.xml".
biodb.DEBUG[2025-07-26 16:03:49.564][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:03:49.567][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-07-26 16:03:49.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:49.572][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:49.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:49.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:49.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:49.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:49.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:03:49.600][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.602][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.604][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.618][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:49.619][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:49.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.622][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.624][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:49.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:49.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.629][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:49.630][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:49.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.633][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.635][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:49.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:49.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.640][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:49.641][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:49.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.644][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.646][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:49.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:49.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.651][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:49.653][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:49.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.655][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.657][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:49.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:49.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.662][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.664][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.666][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.670][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:49.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.679][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.687][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:49.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:49.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.694][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:49.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:49.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.708][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:49.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:49.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:49.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:49.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:49.746][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3002.
biodb.TRACE[2025-07-26 16:03:49.749][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:49.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:49.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.754][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:49.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:49.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.759][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.764][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:49.769][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:49.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:49.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:49.774][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-07-26 16:03:49.775][private$loadEntries] Creating entries from ids [1]: "CCDS9633.1".
biodb.DEBUG[2025-07-26 16:03:49.814][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-07-26 16:03:49.828][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS9633.1".
biodb.TRACE[2025-07-26 16:03:49.830][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-07-26 16:03:49.832][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-07-26 16:03:49.833][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-07-26 16:03:49.834][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-07-26 16:03:49.836][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-07-26 16:03:49.837][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-07-26 16:03:49.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:49.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:49.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:49.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:49.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:49.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:49.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:49.864][scheduler$sendRequest] Getting content of get URL request "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.DEBUG[2025-07-26 16:03:49.867][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:49.869][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:49.870][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-07-26 16:03:50.007][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-07-26 16:03:50.074][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:50.076][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:50.077][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:50.079][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-07-26 16:03:50.196][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-07-26 16:03:50.263][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:50.265][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:50.266][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:50.268][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-07-26 16:03:50.411][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-07-26 16:03:50.482][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:50.484][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:50.485][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:50.486][rule$waitAsNeeded] Wait 0.383998 second(s).
biodb.TRACE[2025-07-26 16:03:50.884][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-07-26 16:03:51.002][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-07-26 16:03:51.076][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:51.077][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:51.079][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:51.080][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-07-26 16:03:51.199][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-07-26 16:03:51.270][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:51.271][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:51.272][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:51.274][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-07-26 16:03:51.402][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-07-26 16:03:51.472][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:51.473][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:51.474][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:51.476][rule$waitAsNeeded] Wait 0.407512 second(s).
biodb.TRACE[2025-07-26 16:03:51.886][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-07-26 16:03:52.010][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-07-26 16:03:52.084][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:52.085][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:52.087][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:52.088][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-07-26 16:03:52.233][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-07-26 16:03:52.299][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:52.301][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:52.302][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:52.304][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-07-26 16:03:52.453][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-07-26 16:03:52.517][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:52.519][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:52.520][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:52.521][rule$waitAsNeeded] Wait 0.363835 second(s).
biodb.TRACE[2025-07-26 16:03:52.888][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-07-26 16:03:53.030][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-07-26 16:03:53.094][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.TRACE[2025-07-26 16:03:53.107][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS9633.1.html"
biodb.DEBUG[2025-07-26 16:03:53.109][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-07-26 16:03:53.111][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:03:53.112][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-07-26 16:03:53.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:53.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:53.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:53.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:53.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:53.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:53.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:03:53.129][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.133][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:53.168][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-07-26 16:03:53.169][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.TRACE[2025-07-26 16:03:53.178][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:03:53.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:03:53.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.183][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:03:53.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:03:53.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.202][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:03:53.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:03:53.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.207][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:03:53.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:03:53.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.223][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:53.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:53.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.265][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:53.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:53.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.270][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:53.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:53.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.274][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:53.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:53.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.302][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.304][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.306][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.322][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:53.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:53.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.327][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:53.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:53.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.332][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:53.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:53.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.337][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:53.338][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:53.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.341][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.342][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:53.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:53.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.356][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:53.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:53.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.361][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:53.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:53.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.366][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:53.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:53.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.371][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:53.372][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:53.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.375][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.376][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:53.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:53.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.390][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.395][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.400][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.405][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.406][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.409][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.410][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.424][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.429][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.434][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.439][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.440][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.443][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.444][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.458][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:53.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:53.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.463][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:53.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:53.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.468][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:53.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:53.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.473][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:53.474][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:53.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.477][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.478][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:53.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:53.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.492][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:53.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:53.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:03:53.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:53.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:03:53.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:53.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.507][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:53.509][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:53.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.511][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.512][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:53.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:53.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.527][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:53.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:53.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.532][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:53.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:53.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.537][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:53.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:53.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.541][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:53.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:53.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.546][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.551][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.556][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:53.561][private$computeField] Compute value for field "aa.seq".
biodb.TRACE[2025-07-26 16:03:53.562][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:53.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:53.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.567][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:53.569][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:53.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.571][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.572][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:53.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:53.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.607][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:53.609][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:53.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.611][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.618][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.620][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.622][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.629][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:53.630][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:53.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.633][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.640][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:53.641][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:53.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.644][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.651][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:03:53.652][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:53.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.655][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.662][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.663][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.666][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.673][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.674][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.677][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.708][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-3627-content.xml".
biodb.DEBUG[2025-07-26 16:03:53.710][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:03:53.711][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-07-26 16:03:53.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:53.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:53.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:53.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:53.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:53.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:53.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:03:53.745][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.747][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.749][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.758][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:53.759][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:53.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.761][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.764][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:53.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:53.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.769][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:53.771][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:53.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.773][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.776][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:53.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:53.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.781][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:53.782][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:53.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.784][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.788][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:53.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:53.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.793][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:53.794][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:53.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.796][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.800][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:53.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:53.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.805][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.806][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.808][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.814][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:53.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.822][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.828][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:53.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:53.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.832][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:53.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:53.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.842][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:53.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:53.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:53.877][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3627.
biodb.TRACE[2025-07-26 16:03:53.880][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:53.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:53.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.884][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:53.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:53.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.889][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.894][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.899][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:53.904][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-07-26 16:03:53.905][private$loadEntries] Creating entries from ids [1]: "CCDS43240.1".
biodb.DEBUG[2025-07-26 16:03:53.907][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-07-26 16:03:53.908][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS43240.1".
biodb.TRACE[2025-07-26 16:03:53.910][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:03:53.913][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS43240.1.html".
biodb.DEBUG[2025-07-26 16:03:53.914][conn$getEntryContent] 1 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-07-26 16:03:53.915][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:03:53.917][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-07-26 16:03:53.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:53.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:53.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:53.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:53.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:53.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:53.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:03:53.934][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.939][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:53.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:53.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:53.973][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-07-26 16:03:53.974][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.TRACE[2025-07-26 16:03:53.975][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:03:53.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:03:53.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.980][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:03:53.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:03:53.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.985][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:03:53.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:03:53.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.990][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:03:53.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:03:53.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:53.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:53.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:53.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.008][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:54.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:54.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.050][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:54.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:54.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.054][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:54.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:54.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.059][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:54.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:54.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.087][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.088][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.091][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.106][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:54.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:54.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.111][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:54.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:54.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.116][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:54.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:54.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.121][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:54.122][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:54.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.125][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.126][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:54.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:54.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.140][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:54.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:54.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.145][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:54.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:54.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.150][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:54.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:54.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.155][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:54.156][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:54.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.159][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.160][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:54.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:54.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.175][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.180][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.185][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.190][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.191][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.193][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.195][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.209][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.215][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.220][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.224][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.226][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.234][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.235][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.249][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:54.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:54.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.254][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:54.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:54.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.259][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:54.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:54.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.264][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:54.265][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:54.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.267][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.269][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:54.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:54.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.283][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:54.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:54.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.289][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:03:54.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:54.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.294][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:03:54.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:54.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.299][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:54.300][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:54.301][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.302][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.304][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:54.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:54.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.318][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:54.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:54.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.323][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:54.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:54.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.329][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:54.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:54.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.333][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:54.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:54.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.338][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.343][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.348][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:54.353][private$computeField] Compute value for field "aa.seq".
biodb.TRACE[2025-07-26 16:03:54.355][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:54.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:54.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.360][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:54.361][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:54.362][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.363][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.364][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:54.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:54.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.399][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:54.401][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:54.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.403][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.410][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.411][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.414][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.421][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:54.422][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:54.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.424][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.431][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:54.432][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:54.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.435][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.441][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:03:54.443][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:54.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.445][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.452][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.453][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.456][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.463][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.464][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.467][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.485][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[2025-07-26 16:03:54.487][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:03:54.489][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-07-26 16:03:54.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:54.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:54.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:54.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:54.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:54.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:54.503][FUN] Functions in observer BiodbConfig: [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[2025-07-26 16:03:54.519][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.520][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.523][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.531][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:54.532][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:54.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.534][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.537][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:54.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:54.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.542][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:54.543][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:54.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.546][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.548][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:54.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:54.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.553][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:54.554][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:54.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.557][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.559][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:54.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:54.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.564][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:54.566][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:54.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.568][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.571][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:54.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:54.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.576][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.577][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.579][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.583][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:54.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.591][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.596][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:54.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:54.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.601][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:54.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:54.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.611][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:54.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:54.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:54.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:54.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:54.645][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 4316.
biodb.TRACE[2025-07-26 16:03:54.648][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:54.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:54.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.653][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:54.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:54.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.658][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.662][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:54.667][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:54.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:54.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:54.672][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-07-26 16:03:54.673][private$loadEntries] Creating entries from ids [1]: "CCDS8317.1".
biodb.DEBUG[2025-07-26 16:03:54.675][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-07-26 16:03:54.677][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS8317.1".
biodb.TRACE[2025-07-26 16:03:54.678][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-07-26 16:03:54.680][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-07-26 16:03:54.681][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-07-26 16:03:54.682][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-07-26 16:03:54.683][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-07-26 16:03:54.685][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-07-26 16:03:54.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:54.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:54.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:54.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:54.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:54.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:54.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:54.702][scheduler$sendRequest] Getting content of get URL request "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.DEBUG[2025-07-26 16:03:54.705][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:54.707][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:54.708][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-07-26 16:03:54.827][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-07-26 16:03:54.898][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:54.900][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:54.901][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:54.902][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-07-26 16:03:55.030][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-07-26 16:03:55.102][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:55.103][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:55.104][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:55.106][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-07-26 16:03:55.235][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-07-26 16:03:55.306][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:55.308][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:55.309][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:55.311][rule$waitAsNeeded] Wait 0.39771 second(s).
biodb.TRACE[2025-07-26 16:03:55.725][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-07-26 16:03:55.854][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-07-26 16:03:55.928][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:55.930][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:55.931][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:55.932][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-07-26 16:03:56.100][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-07-26 16:03:56.169][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:56.170][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:56.171][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:56.173][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-07-26 16:03:56.299][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-07-26 16:03:56.372][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:56.374][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:56.375][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:56.376][rule$waitAsNeeded] Wait 0.347329 second(s).
biodb.TRACE[2025-07-26 16:03:56.727][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-07-26 16:03:56.853][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-07-26 16:03:56.919][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:56.921][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:56.922][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:56.924][rule$waitAsNeeded] Wait 0.00883913 second(s).
biodb.TRACE[2025-07-26 16:03:56.946][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-07-26 16:03:57.073][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-07-26 16:03:57.144][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:57.146][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:57.147][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:57.148][rule$waitAsNeeded] Wait 0.0245891 second(s).
biodb.TRACE[2025-07-26 16:03:57.181][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-07-26 16:03:57.303][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-07-26 16:03:57.375][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:57.376][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:57.378][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:57.379][rule$waitAsNeeded] Wait 0.347423 second(s).
biodb.TRACE[2025-07-26 16:03:57.730][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-07-26 16:03:57.853][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-07-26 16:03:57.917][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.TRACE[2025-07-26 16:03:57.920][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS8317.1.html"
biodb.DEBUG[2025-07-26 16:03:57.923][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-07-26 16:03:57.924][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:03:57.926][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-07-26 16:03:57.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:57.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:57.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:57.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:57.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:57.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:57.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:03:57.942][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:57.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:57.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:57.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:57.947][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:57.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:57.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:57.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:57.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:57.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:57.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:57.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:57.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:57.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:57.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:57.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:57.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:57.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:57.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:57.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:57.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:57.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:57.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:57.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:57.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:57.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:57.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:57.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:57.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:57.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:57.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:57.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:57.981][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-07-26 16:03:57.982][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.TRACE[2025-07-26 16:03:57.984][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:03:57.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:03:57.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:57.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:57.988][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:03:57.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:03:57.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:57.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:57.993][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:03:57.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:03:57.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:57.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:57.998][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:03:57.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:03:58.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.014][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:58.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:58.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.056][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:58.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:58.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.061][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:58.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:58.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.066][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:58.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:58.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.094][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.095][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.097][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.113][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:58.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:58.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.118][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:58.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:58.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.123][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:58.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:58.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.128][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:58.129][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:58.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.132][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.133][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:58.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:58.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.148][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:58.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:58.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.156][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:58.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:58.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.164][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:58.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:58.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.171][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:58.173][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:58.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.177][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.179][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:58.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:58.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.198][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.203][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.208][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.213][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.214][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.217][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.218][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.233][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.238][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.242][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.247][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.249][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.251][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.252][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.267][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:58.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:58.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.272][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:58.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:58.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.277][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:58.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:58.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.281][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:58.283][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:58.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.285][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.286][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:58.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:58.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.301][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:58.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:58.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.306][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:03:58.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:58.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:03:58.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:58.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.315][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:58.317][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:58.318][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.319][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.320][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:58.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:58.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.335][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:58.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:58.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.340][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:58.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:58.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.345][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:58.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:58.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.350][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:58.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:58.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.354][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.359][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.364][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:58.380][private$computeField] Compute value for field "aa.seq".
biodb.TRACE[2025-07-26 16:03:58.381][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:58.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:58.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.386][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:58.387][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:58.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.389][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.391][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:03:58.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:58.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.425][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:58.426][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:58.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.429][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.436][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.437][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.440][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.447][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:58.448][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:58.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.450][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.457][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:58.459][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:58.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.461][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.468][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:03:58.469][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:58.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.471][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.478][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.480][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.482][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.489][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.490][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.493][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.528][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[2025-07-26 16:03:58.530][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:03:58.532][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-07-26 16:03:58.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:58.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:58.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:58.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:58.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:58.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:58.546][FUN] Functions in observer BiodbConfig: [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[2025-07-26 16:03:58.578][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.580][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.581][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.582][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.591][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:58.593][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:58.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.595][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.599][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:03:58.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:03:58.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.604][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:58.605][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:58.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.608][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.612][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:03:58.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:03:58.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.617][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:58.618][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:58.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.621][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.625][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:03:58.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:03:58.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.630][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:58.631][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:58.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.634][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.638][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:03:58.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:03:58.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.643][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.644][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.647][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.655][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:03:58.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.668][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.673][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:58.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:58.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.678][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:58.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:58.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.688][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:58.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:03:58.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:03:58.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:03:58.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:58.722][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 50943.
biodb.TRACE[2025-07-26 16:03:58.725][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:58.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:58.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.729][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:03:58.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:03:58.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.736][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.743][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:03:58.750][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:03:58.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:03:58.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:03:58.755][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-07-26 16:03:58.757][private$loadEntries] Creating entries from ids [1]: "CCDS14323.1".
biodb.DEBUG[2025-07-26 16:03:58.758][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-07-26 16:03:58.760][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS14323.1".
biodb.TRACE[2025-07-26 16:03:58.762][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-07-26 16:03:58.763][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-07-26 16:03:58.764][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-07-26 16:03:58.766][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-07-26 16:03:58.767][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-07-26 16:03:58.768][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-07-26 16:03:58.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:03:58.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:03:58.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:03:58.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:03:58.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:03:58.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:03:58.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:03:58.785][scheduler$sendRequest] Getting content of get URL request "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.DEBUG[2025-07-26 16:03:58.788][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:58.790][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:58.791][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-07-26 16:03:58.921][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-07-26 16:03:58.996][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:58.998][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:58.999][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:59.000][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-07-26 16:03:59.123][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-07-26 16:03:59.192][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:59.194][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:59.195][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:03:59.197][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-07-26 16:03:59.317][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-07-26 16:03:59.393][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:59.395][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:59.396][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:59.397][rule$waitAsNeeded] Wait 0.393686 second(s).
biodb.TRACE[2025-07-26 16:03:59.797][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-07-26 16:03:59.922][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-07-26 16:03:59.995][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:03:59.996][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:03:59.997][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:03:59.999][rule$waitAsNeeded] Wait 0.00149798 second(s).
biodb.TRACE[2025-07-26 16:04:00.016][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-07-26 16:04:00.137][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-07-26 16:04:00.203][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:00.205][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:00.206][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:00.208][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-07-26 16:04:00.334][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-07-26 16:04:00.414][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:00.415][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:00.416][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:00.418][rule$waitAsNeeded] Wait 0.3784 second(s).
biodb.TRACE[2025-07-26 16:04:00.799][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-07-26 16:04:00.941][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-07-26 16:04:01.013][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:01.015][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:01.016][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:01.017][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-07-26 16:04:01.138][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-07-26 16:04:01.217][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:01.218][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:01.220][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:01.221][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-07-26 16:04:01.346][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-07-26 16:04:01.416][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:01.417][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:01.418][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:01.420][rule$waitAsNeeded] Wait 0.378936 second(s).
biodb.TRACE[2025-07-26 16:04:01.801][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-07-26 16:04:01.926][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-07-26 16:04:01.999][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.TRACE[2025-07-26 16:04:02.002][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS14323.1.html"
biodb.DEBUG[2025-07-26 16:04:02.004][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-07-26 16:04:02.005][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:04:02.007][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-07-26 16:04:02.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:02.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:02.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:02.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:02.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:02.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:02.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:02.024][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.028][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:02.063][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-07-26 16:04:02.070][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.TRACE[2025-07-26 16:04:02.080][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:02.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:02.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.085][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:02.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:02.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.090][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:02.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:02.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.095][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:02.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:02.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.111][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:02.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:02.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.153][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:02.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:02.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.158][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:02.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:02.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.163][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:02.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:02.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.191][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.192][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.194][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.210][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:02.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:02.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.216][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:02.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:02.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.220][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:02.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:02.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.225][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:02.227][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:02.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.229][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.230][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:02.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:02.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.245][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:02.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:02.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.250][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:02.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:02.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.255][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:02.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:02.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.260][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:02.261][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:02.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.263][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.265][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:02.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:02.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.279][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.284][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.289][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.294][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.295][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.298][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.299][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.319][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.324][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.329][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.334][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.335][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.337][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.339][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.353][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:02.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:02.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.358][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:02.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:02.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.363][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:02.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:02.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.368][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:02.369][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:02.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.372][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.373][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:02.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:02.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.387][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:02.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:02.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:02.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:02.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.397][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:02.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:02.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.402][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:02.404][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:02.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.406][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.407][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:02.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:02.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.421][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:04:02.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:02.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.426][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:02.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:02.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.431][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:02.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:02.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.436][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:02.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:02.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.441][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.446][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.451][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:02.456][private$computeField] Compute value for field "aa.seq".
biodb.TRACE[2025-07-26 16:04:02.457][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:02.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:02.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.462][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:04:02.463][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:02.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.465][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.467][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:04:02.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:02.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.501][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:02.503][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:02.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.505][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.512][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.514][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.516][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.523][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:02.524][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:02.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.526][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.533][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:02.534][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:02.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.537][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.543][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:02.545][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:02.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.547][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.554][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.555][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.558][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.572][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.574][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.576][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.592][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-5551-content.xml".
biodb.DEBUG[2025-07-26 16:04:02.594][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:04:02.595][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-07-26 16:04:02.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:02.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:02.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:02.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:02.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:02.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:02.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:02.619][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.620][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.623][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.630][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:02.631][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:02.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.633][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.636][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:02.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:02.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.640][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:02.642][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:02.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.644][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.646][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:02.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:02.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.651][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:02.652][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:02.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.655][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.657][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:02.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:02.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.662][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:02.663][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:02.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.666][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.668][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:02.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:02.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.673][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.674][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.676][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.680][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:02.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.686][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.692][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:02.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:02.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.696][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:02.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:02.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.706][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:02.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:02.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:02.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:02.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:02.743][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 5551.
biodb.TRACE[2025-07-26 16:04:02.745][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:02.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:02.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.750][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:02.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:02.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.755][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.760][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:02.765][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:02.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:02.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:02.770][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-07-26 16:04:02.771][private$loadEntries] Creating entries from ids [1]: "CCDS7305.1".
biodb.DEBUG[2025-07-26 16:04:02.773][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-07-26 16:04:02.774][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS7305.1".
biodb.TRACE[2025-07-26 16:04:02.776][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-07-26 16:04:02.778][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-07-26 16:04:02.779][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-07-26 16:04:02.780][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-07-26 16:04:02.781][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-07-26 16:04:02.782][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-07-26 16:04:02.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:02.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:02.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:02.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:02.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:02.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:02.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:02.800][scheduler$sendRequest] Getting content of get URL request "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.DEBUG[2025-07-26 16:04:02.803][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:02.804][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:02.806][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-07-26 16:04:02.932][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-07-26 16:04:02.997][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:02.999][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:03.000][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:03.001][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-07-26 16:04:03.132][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-07-26 16:04:03.204][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:03.206][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:03.207][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:03.209][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-07-26 16:04:03.354][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-07-26 16:04:03.419][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:03.421][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:03.422][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:03.424][rule$waitAsNeeded] Wait 0.382196 second(s).
biodb.TRACE[2025-07-26 16:04:03.822][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-07-26 16:04:03.941][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-07-26 16:04:04.004][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:04.006][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:04.007][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:04.009][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-07-26 16:04:04.127][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-07-26 16:04:04.211][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:04.212][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:04.213][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:04.215][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-07-26 16:04:04.341][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-07-26 16:04:04.437][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:04.438][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:04.439][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:04.441][rule$waitAsNeeded] Wait 0.380744 second(s).
biodb.TRACE[2025-07-26 16:04:04.824][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-07-26 16:04:04.949][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-07-26 16:04:05.023][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:05.024][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:05.025][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:05.027][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-07-26 16:04:05.150][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-07-26 16:04:05.221][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:05.222][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:05.223][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:05.225][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-07-26 16:04:05.374][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-07-26 16:04:05.437][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:05.438][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:05.439][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:05.441][rule$waitAsNeeded] Wait 0.383324 second(s).
biodb.TRACE[2025-07-26 16:04:05.827][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-07-26 16:04:05.957][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-07-26 16:04:06.041][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.TRACE[2025-07-26 16:04:06.044][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS7305.1.html"
biodb.DEBUG[2025-07-26 16:04:06.046][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-07-26 16:04:06.048][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:04:06.049][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-07-26 16:04:06.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:06.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:06.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:06.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:06.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:06.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:06.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:06.067][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.072][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:06.106][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-07-26 16:04:06.107][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.TRACE[2025-07-26 16:04:06.108][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:06.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:06.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.113][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:06.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:06.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.118][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:06.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:06.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.123][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:06.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:06.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.140][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:06.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:06.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.182][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:06.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:06.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.187][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:06.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:06.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.192][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:06.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:06.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.219][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.221][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.223][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.253][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:06.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:06.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.258][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:06.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:06.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.263][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:06.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:06.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.268][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:06.269][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:06.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.272][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.273][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:06.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:06.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.287][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:06.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:06.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.292][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:06.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:06.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.297][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:06.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:06.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.302][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:06.303][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:06.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.306][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.307][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:06.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:06.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.322][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.327][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.332][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.337][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.338][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.341][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.342][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.357][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.362][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.367][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.372][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.374][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.376][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.377][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.392][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:06.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:06.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.397][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:06.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:06.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.402][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:06.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:06.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.407][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:06.408][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:06.409][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.411][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.412][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:06.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:06.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.427][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:06.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:06.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.432][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:06.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:06.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:06.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:06.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.442][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:06.443][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:06.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.446][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.447][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:06.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:06.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.462][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:04:06.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:06.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.467][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:06.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:06.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.472][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:06.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:06.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.477][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:06.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:06.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.482][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.487][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.491][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:06.496][private$computeField] Compute value for field "aa.seq".
biodb.TRACE[2025-07-26 16:04:06.498][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:06.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:06.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.502][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:04:06.504][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:06.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.506][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.507][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:04:06.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:06.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.543][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:06.544][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:06.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.546][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.553][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.555][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.557][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.564][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:06.565][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:06.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.567][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.574][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:06.576][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:06.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.578][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.585][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:06.586][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:06.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.588][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.595][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.597][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.599][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.606][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.607][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.609][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.625][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-916-content.xml".
biodb.DEBUG[2025-07-26 16:04:06.627][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:04:06.628][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-07-26 16:04:06.630][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:06.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:06.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:06.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:06.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:06.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:06.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:06.652][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.654][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.656][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.669][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:06.671][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:06.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.675][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.678][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:06.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:06.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.685][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:06.687][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:06.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.691][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.694][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:06.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:06.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.702][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:06.704][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:06.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.708][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.711][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:06.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:06.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.718][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:06.720][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:06.722][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.723][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.727][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:06.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:06.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.735][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.737][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.740][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.745][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:06.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.752][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.758][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:06.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:06.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.762][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:06.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:06.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.772][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:06.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:06.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:06.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:06.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:06.812][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 916.
biodb.TRACE[2025-07-26 16:04:06.814][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:06.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:06.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.819][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:06.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:06.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.824][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.829][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:06.833][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:06.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:06.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:06.838][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-07-26 16:04:06.839][private$loadEntries] Creating entries from ids [1]: "CCDS31685.1".
biodb.DEBUG[2025-07-26 16:04:06.840][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-07-26 16:04:06.842][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS31685.1".
biodb.TRACE[2025-07-26 16:04:06.844][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-07-26 16:04:06.845][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-07-26 16:04:06.847][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-07-26 16:04:06.848][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-07-26 16:04:06.849][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-07-26 16:04:06.851][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-07-26 16:04:06.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:06.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:06.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:06.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:06.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:06.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:06.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:06.868][scheduler$sendRequest] Getting content of get URL request "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.DEBUG[2025-07-26 16:04:06.871][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:06.872][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:06.874][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-07-26 16:04:07.004][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-07-26 16:04:07.075][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:07.076][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:07.077][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:07.079][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-07-26 16:04:07.200][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-07-26 16:04:07.270][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:07.271][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:07.273][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:07.274][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-07-26 16:04:07.414][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-07-26 16:04:07.478][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:07.479][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:07.480][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:07.482][rule$waitAsNeeded] Wait 0.39205 second(s).
biodb.TRACE[2025-07-26 16:04:07.878][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-07-26 16:04:07.999][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-07-26 16:04:08.068][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:08.069][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:08.070][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:08.072][rule$waitAsNeeded] Wait 0.00728989 second(s).
biodb.TRACE[2025-07-26 16:04:08.082][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-07-26 16:04:08.206][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-07-26 16:04:08.281][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:08.283][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:08.284][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:08.286][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-07-26 16:04:08.406][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-07-26 16:04:08.484][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:08.486][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:08.487][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:08.488][rule$waitAsNeeded] Wait 0.389564 second(s).
biodb.TRACE[2025-07-26 16:04:08.881][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-07-26 16:04:09.023][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-07-26 16:04:09.087][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:09.088][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:09.089][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:09.091][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-07-26 16:04:09.219][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-07-26 16:04:09.295][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:09.297][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:09.298][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:09.300][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-07-26 16:04:09.450][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-07-26 16:04:09.532][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:09.533][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:09.535][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:09.536][rule$waitAsNeeded] Wait 0.344396 second(s).
biodb.TRACE[2025-07-26 16:04:09.883][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-07-26 16:04:10.013][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-07-26 16:04:10.098][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1". Retrying connection to server...
biodb.TRACE[2025-07-26 16:04:10.101][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS31685.1.html"
biodb.DEBUG[2025-07-26 16:04:10.104][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-07-26 16:04:10.106][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:04:10.108][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-07-26 16:04:10.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:10.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:10.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:10.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:10.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:10.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:10.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:10.126][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.131][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:10.165][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-07-26 16:04:10.166][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.TRACE[2025-07-26 16:04:10.168][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:10.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:10.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.172][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:10.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:10.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.177][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:10.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:10.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.182][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:10.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:10.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.199][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.241][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.246][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.251][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.278][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.279][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.282][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.297][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:10.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.302][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.307][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.312][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:10.313][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.316][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.317][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:10.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.332][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:10.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:10.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.337][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:10.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:10.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.342][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:10.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:10.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.346][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:10.348][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:10.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.350][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.351][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:10.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:10.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.366][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:10.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:10.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.371][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:10.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:10.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.376][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:10.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:10.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.381][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:10.382][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:10.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.385][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.386][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:10.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:10.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.401][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.420][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.425][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.430][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.431][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.433][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.435][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.449][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:10.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:10.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.454][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:10.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:10.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.459][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:10.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:10.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.464][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:10.465][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:10.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.467][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.469][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:10.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:10.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:10.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:10.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.488][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:10.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:10.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:10.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:10.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.498][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:10.499][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:10.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.502][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.503][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:10.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:10.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.518][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:04:10.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:10.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.523][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:10.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:10.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.528][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:10.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:10.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.533][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:10.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:10.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.538][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.543][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.547][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:10.552][private$computeField] Compute value for field "aa.seq".
biodb.TRACE[2025-07-26 16:04:10.554][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:10.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:10.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.558][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:04:10.560][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:10.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.562][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.563][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-07-26 16:04:10.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:10.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.598][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:10.599][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:10.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.602][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.609][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.610][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.612][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.619][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:10.620][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:10.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.623][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.629][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.631][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.633][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.639][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:10.641][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:10.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.643][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.650][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.651][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.653][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.660][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:10.661][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:10.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.664][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.671][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[2025-07-26 16:04:10.673][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:04:10.675][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-07-26 16:04:10.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:10.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:10.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:10.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:10.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:10.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:10.689][FUN] Functions in observer BiodbConfig: [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[2025-07-26 16:04:10.691][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.693][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.695][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.701][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:10.703][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:10.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.705][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.706][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:10.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:10.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.711][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:10.713][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:10.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.715][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.716][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:10.718][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.720][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.721][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:10.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.726][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:10.728][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:10.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.730][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.732][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:10.733][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:10.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.735][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.737][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.742][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.752][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:10.786][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 9606.
biodb.TRACE[2025-07-26 16:04:10.788][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:10.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:10.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.793][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:10.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:10.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.798][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:10.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.803][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:10.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:10.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.808][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:10.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:10.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.813][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:10.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:10.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.817][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:10.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:10.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.834][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.875][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.881][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.885][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:10.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.919][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.921][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.923][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:10.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:10.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.939][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:10.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.944][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.949][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.953][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:10.955][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.957][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.958][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:10.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:10.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.973][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:10.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:10.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.978][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:10.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:10.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.983][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:10.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:10.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.988][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:10.989][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:10.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.991][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:10.993][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:10.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:10.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:10.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:11.007][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:11.008][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:11.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:11.011][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:11.018][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:11.019][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:11.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:11.021][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:11.028][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:11.030][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:11.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:11.032][ef$get] fields variable is a list.
biodb.INFO [2025-07-26 16:04:11.044][biodb::testThat]
biodb.INFO [2025-07-26 16:04:11.046][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-07-26 16:04:11.047][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:11.048][biodb::testThat]
biodb.DEBUG[2025-07-26 16:04:11.051][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2025-07-26 16:04:11.052][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
biodb.TRACE[2025-07-26 16:04:11.054][cch$loadFileContent] Trying to load 8 files from cache: [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.TRACE[2025-07-26 16:04:11.057][cch$loadFileContent] file.exist = [8]: "FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE".
biodb.TRACE[2025-07-26 16:04:11.278][loadFileContents] Loaded 7 files from cache: [7]: "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[2025-07-26 16:04:11.280][conn$getEntryContent] 7 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-07-26 16:04:11.281][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-07-26 16:04:11.282][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-07-26 16:04:11.283][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-07-26 16:04:11.285][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.DEBUG[2025-07-26 16:04:11.292][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.DEBUG[2025-07-26 16:04:11.294][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:11.295][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:11.297][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-07-26 16:04:11.455][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-07-26 16:04:11.525][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=gene&id=2833&retmode=xml When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:11.526][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:11.528][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:11.529][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-07-26 16:04:11.653][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-07-26 16:04:11.722][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=gene&id=2833&retmode=xml When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:11.724][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:11.725][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:11.726][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-07-26 16:04:11.857][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-07-26 16:04:11.927][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=gene&id=2833&retmode=xml When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:11.928][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:11.930][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:11.931][rule$waitAsNeeded] Wait 0.365453 second(s).
biodb.TRACE[2025-07-26 16:04:12.310][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-07-26 16:04:12.435][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-07-26 16:04:12.505][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=gene&id=2833&retmode=xml When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:12.506][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:12.507][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:12.509][rule$waitAsNeeded] Wait 0.0203331 second(s).
biodb.TRACE[2025-07-26 16:04:12.546][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-07-26 16:04:12.690][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-07-26 16:04:12.771][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=gene&id=2833&retmode=xml When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:12.772][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:12.773][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:12.775][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-07-26 16:04:12.910][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-07-26 16:04:12.974][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=gene&id=2833&retmode=xml When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:12.975][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:12.976][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:12.978][rule$waitAsNeeded] Wait 0.33208 second(s).
biodb.TRACE[2025-07-26 16:04:13.313][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-07-26 16:04:13.443][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-07-26 16:04:13.523][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=gene&id=2833&retmode=xml When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:13.525][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:13.526][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:13.527][rule$waitAsNeeded] Wait 0.0179429 second(s).
biodb.TRACE[2025-07-26 16:04:13.548][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-07-26 16:04:13.677][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-07-26 16:04:13.745][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=gene&id=2833&retmode=xml When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:13.746][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:13.748][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:13.749][rule$waitAsNeeded] Wait 0.0259631 second(s).
biodb.TRACE[2025-07-26 16:04:13.783][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-07-26 16:04:13.913][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-07-26 16:04:13.995][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=gene&id=2833&retmode=xml When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:13.997][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:13.998][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:13.999][rule$waitAsNeeded] Wait 0.313315 second(s).
biodb.TRACE[2025-07-26 16:04:14.315][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-07-26 16:04:14.436][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-07-26 16:04:14.507][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=gene&id=2833&retmode=xml When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:14.509][private$checkXml] XML contains error messages. At least one of the IDs to retrieve is wrong.
biodb.TRACE[2025-07-26 16:04:14.512][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/2833.xml"
biodb.DEBUG[2025-07-26 16:04:14.514][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-07-26 16:04:14.516][self$createEntryFromContent] Creating NCBI Gene entries from 8 content(s).
biodb.DEBUG[2025-07-26 16:04:14.517][self$createEntryFromContent] Parsing 8 NCBI Gene entries.
biodb.DEBUG[2025-07-26 16:04:14.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:14.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:14.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:14.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:14.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:14.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:14.531][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.TRACE[2025-07-26 16:04:14.533][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.538][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:14.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:14.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:14.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:14.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:14.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:14.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:14.561][FUN] Functions in observer BiodbConfig: [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[2025-07-26 16:04:14.575][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.576][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.578][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.586][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:14.587][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:14.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.589][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.592][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:14.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:14.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.597][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:14.598][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:14.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.600][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.603][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:14.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:14.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.608][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:14.609][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:14.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.612][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.614][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:14.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:14.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.619][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:14.620][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:14.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.623][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.625][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:14.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:14.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.630][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:14.632][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:14.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.634][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.638][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:14.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:14.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.647][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:14.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:14.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.652][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.657][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.666][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:14.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:14.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:14.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:14.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:14.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:14.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:14.699][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.TRACE[2025-07-26 16:04:14.721][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.723][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.726][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.735][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:14.736][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:14.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.738][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.742][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:14.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:14.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.747][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:14.748][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:14.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.750][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.754][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:14.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:14.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.759][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:14.760][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:14.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.762][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.766][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:14.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:14.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.785][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:14.787][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:14.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.789][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.793][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:14.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:14.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.798][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:14.799][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:14.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.802][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.808][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:14.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:14.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.816][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:14.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:14.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.821][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.826][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.836][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:14.855][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:14.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:14.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:14.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:14.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:14.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:14.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:14.882][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.884][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.886][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.894][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:14.895][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:14.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.897][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.900][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:14.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:14.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.905][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:14.907][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:14.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.909][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.912][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:14.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:14.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.917][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:14.918][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:14.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.920][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.923][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:14.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:14.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.928][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:14.930][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:14.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.932][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.935][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:14.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:14.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.940][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:14.941][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:14.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.943][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.948][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:14.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:14.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.955][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:14.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:14.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.960][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.965][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.975][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:14.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:14.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:14.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:14.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:14.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:14.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:14.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:14.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:15.004][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:15.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:15.006][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:15.007][FUN] Functions in observer BiodbConfig: [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[2025-07-26 16:04:15.040][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.041][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.044][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.053][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:15.055][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:15.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.057][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.062][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:15.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:15.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.067][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:15.068][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:15.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.070][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.075][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:15.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:15.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.080][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:15.081][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:15.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.084][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.088][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:15.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:15.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.094][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:15.095][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:15.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.097][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.102][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:15.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:15.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.107][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:15.108][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:15.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.111][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.120][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:15.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:15.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.134][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:15.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:15.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.139][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.144][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.154][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:15.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:15.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:15.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:15.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:15.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:15.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:15.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:15.197][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.199][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.201][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.208][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:15.210][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:15.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.212][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.214][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:15.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:15.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.219][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:15.221][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:15.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.223][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.225][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:15.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:15.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.230][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:15.232][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:15.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.234][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.236][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:15.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:15.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.241][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:15.243][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:15.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.245][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.247][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:15.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:15.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.252][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:15.253][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:15.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.256][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.259][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:15.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:15.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.266][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:15.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:15.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.271][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.276][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.286][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:15.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:15.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:15.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:15.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:15.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:15.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:15.318][FUN] Functions in observer BiodbConfig: [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[2025-07-26 16:04:15.329][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.330][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.333][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.340][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:15.341][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:15.343][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.344][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.346][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:15.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:15.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.351][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:15.352][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:15.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.355][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.357][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:15.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:15.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.362][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:15.363][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:15.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.366][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.368][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:15.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:15.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.373][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:15.374][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:15.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.377][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.379][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:15.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:15.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.390][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:15.391][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:15.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.393][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.397][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:15.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:15.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.404][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:15.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:15.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.409][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.413][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.423][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:15.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:15.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:15.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:15.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:15.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:15.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:15.455][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.TRACE[2025-07-26 16:04:15.458][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.459][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.461][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.468][ef$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:15.469][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:15.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.471][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.473][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-07-26 16:04:15.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-07-26 16:04:15.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.478][ef$get] Asked field names are: location.
biodb.TRACE[2025-07-26 16:04:15.479][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-07-26 16:04:15.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.481][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.483][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:15.484][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:15.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.487][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.488][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-07-26 16:04:15.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-07-26 16:04:15.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.493][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-07-26 16:04:15.494][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:15.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.497][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.498][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:15.499][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-07-26 16:04:15.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.502][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.503][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.508][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.518][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-07-26 16:04:15.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:15.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:15.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:15.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:15.665][self$createEntryFromContent] Accession numbers: NA, 3002, 3627, 4316, 50943, 5551, 916, 9606.
biodb.DEBUG[2025-07-26 16:04:15.666][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-07-26 16:04:15.681][biodb::testThat]
biodb.INFO [2025-07-26 16:04:15.682][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-07-26 16:04:15.683][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:15.684][biodb::testThat]
biodb.TRACE[2025-07-26 16:04:15.688][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:15.689][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:15.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:15.691][ef$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:15.693][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.INFO [2025-07-26 16:04:15.748][biodb::testThat]
biodb.INFO [2025-07-26 16:04:15.749][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-07-26 16:04:15.750][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:15.751][biodb::testThat]
biodb.INFO [2025-07-26 16:04:15.793][biodb::testThat]
biodb.INFO [2025-07-26 16:04:15.794][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-07-26 16:04:15.795][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:15.796][biodb::testThat]
biodb.INFO [2025-07-26 16:04:15.842][biodb::testThat]
biodb.INFO [2025-07-26 16:04:15.843][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-07-26 16:04:15.844][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:15.845][biodb::testThat]
biodb.INFO [2025-07-26 16:04:15.860][biodb::testThat]
biodb.INFO [2025-07-26 16:04:15.861][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-07-26 16:04:15.862][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:15.863][biodb::testThat]
biodb.INFO [2025-07-26 16:04:15.874][biodb::testThat]
biodb.INFO [2025-07-26 16:04:15.875][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-07-26 16:04:15.876][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:15.877][biodb::testThat]
biodb.DEBUG[2025-07-26 16:04:15.882][function(conn, opt)] Trying to download "https://www.ncbi.nlm.nih.gov/gene?term=2833".
biodb.DEBUG[2025-07-26 16:04:16.004][getUrlContent] Use RCurl for downloading content of URL https://www.ncbi.nlm.nih.gov/gene?term=2833.
biodb.INFO [2025-07-26 16:04:16.092][biodb::testThat]
biodb.INFO [2025-07-26 16:04:16.093][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-07-26 16:04:16.094][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:16.095][biodb::testThat]
biodb.INFO [2025-07-26 16:04:16.104][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-07-26 16:04:16.106][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.gene from the request scheduler
biodb.INFO [2025-07-26 16:04:16.107][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.DEBUG[2025-07-26 16:04:16.109][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.ccds from the request scheduler
biodb.INFO [2025-07-26 16:04:16.116][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-07-26 16:04:16.117][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-07-26 16:04:16.118][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.120][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.123][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-07-26 16:04:16.129][biodb::testContext]
biodb.INFO [2025-07-26 16:04:16.130][biodb::testContext] ********************************************************************************
biodb.INFO [2025-07-26 16:04:16.131][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2025-07-26 16:04:16.133][biodb::testContext] ********************************************************************************
biodb.INFO [2025-07-26 16:04:16.134][biodb::testContext]
biodb.INFO [2025-07-26 16:04:16.136][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-07-26 16:04:16.139][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-07-26 16:04:16.144][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-26 16:04:16.145][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-07-26 16:04:16.147][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-07-26 16:04:16.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.150][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[2025-07-26 16:04:16.151][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-07-26 16:04:16.153][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-07-26 16:04:16.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.157][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-07-26 16:04:16.158][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-07-26 16:04:16.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.161][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[2025-07-26 16:04:16.163][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-07-26 16:04:16.164][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-07-26 16:04:16.165][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-07-26 16:04:16.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.170][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-07-26 16:04:16.171][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-07-26 16:04:16.172][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-07-26 16:04:16.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.177][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-07-26 16:04:16.178][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-07-26 16:04:16.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.182][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-07-26 16:04:16.183][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-07-26 16:04:16.185][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-07-26 16:04:16.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.189][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-07-26 16:04:16.190][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-07-26 16:04:16.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.195][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-07-26 16:04:16.196][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-07-26 16:04:16.197][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-07-26 16:04:16.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.202][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-07-26 16:04:16.203][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-07-26 16:04:16.204][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-07-26 16:04:16.205][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-07-26 16:04:16.207][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-07-26 16:04:16.208][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-07-26 16:04:16.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.212][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-07-26 16:04:16.214][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-07-26 16:04:16.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.218][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-07-26 16:04:16.219][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-07-26 16:04:16.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.224][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-07-26 16:04:16.225][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-07-26 16:04:16.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.230][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-07-26 16:04:16.231][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-07-26 16:04:16.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.235][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-07-26 16:04:16.236][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-07-26 16:04:16.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.240][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[2025-07-26 16:04:16.241][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-07-26 16:04:16.242][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-07-26 16:04:16.245][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-07-26 16:04:16.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.250][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-07-26 16:04:16.251][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-07-26 16:04:16.252][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-07-26 16:04:16.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.257][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-07-26 16:04:16.259][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.260][self$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[2025-07-26 16:04:16.261][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.263][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:16.264][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.265][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.266][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.267][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.269][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-07-26 16:04:16.270][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:16.271][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.272][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-07-26 16:04:16.273][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:16.275][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.276][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.277][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:04:16.277][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-26 16:04:16.277][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-26 16:04:16.277][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-07-26 16:04:16.277][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-07-26 16:04:16.278][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:04:16.280][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.281][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.282][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:16.283][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.284][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.285][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.286][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.288][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:16.289][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:16.290][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.291][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.293][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-07-26 16:04:16.294][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.296][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-07-26 16:04:16.297][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.298][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:16.299][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.301][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.302][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.303][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.304][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-07-26 16:04:16.305][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:16.307][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.308][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-07-26 16:04:16.309][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:16.310][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.312][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.313][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:04:16.313][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-26 16:04:16.313][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-26 16:04:16.313][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-07-26 16:04:16.313][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-07-26 16:04:16.314][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:04:16.315][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.316][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.317][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:16.319][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.320][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.321][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.322][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.323][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:16.324][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:16.326][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.327][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.328][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-07-26 16:04:16.330][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.331][self$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[2025-07-26 16:04:16.333][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.334][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:16.335][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.336][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.337][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.339][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.340][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-07-26 16:04:16.341][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:16.342][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.344][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-07-26 16:04:16.345][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:16.346][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.347][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.348][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.350][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:04:16.351][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.352][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.353][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:16.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.355][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.356][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.358][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.359][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:16.360][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:16.361][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.362][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.364][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-07-26 16:04:16.366][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.367][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-07-26 16:04:16.368][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.369][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:16.370][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.372][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.373][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.374][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.375][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-07-26 16:04:16.377][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:16.378][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.379][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-07-26 16:04:16.380][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:16.382][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.383][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.384][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.385][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:04:16.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.389][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:16.390][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.391][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.392][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.393][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.394][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:16.396][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:16.397][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.398][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.400][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-26 16:04:16.401][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.505][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-07-26 16:04:16.507][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-07-26 16:04:16.508][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-07-26 16:04:16.510][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-07-26 16:04:16.511][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-07-26 16:04:16.513][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-07-26 16:04:16.514][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-07-26 16:04:16.516][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-07-26 16:04:16.517][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-07-26 16:04:16.519][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-07-26 16:04:16.521][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-07-26 16:04:16.522][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-07-26 16:04:16.524][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-07-26 16:04:16.525][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-07-26 16:04:16.527][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-07-26 16:04:16.528][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-07-26 16:04:16.530][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-07-26 16:04:16.531][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-07-26 16:04:16.533][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-07-26 16:04:16.534][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-07-26 16:04:16.536][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-07-26 16:04:16.537][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-07-26 16:04:16.539][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-07-26 16:04:16.541][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-07-26 16:04:16.542][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-07-26 16:04:16.544][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-07-26 16:04:16.545][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-07-26 16:04:16.547][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-07-26 16:04:16.548][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-07-26 16:04:16.550][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-07-26 16:04:16.551][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-07-26 16:04:16.553][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-07-26 16:04:16.555][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-07-26 16:04:16.556][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-07-26 16:04:16.558][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-07-26 16:04:16.559][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-07-26 16:04:16.561][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-07-26 16:04:16.562][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-07-26 16:04:16.564][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-07-26 16:04:16.565][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-07-26 16:04:16.567][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-07-26 16:04:16.569][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-07-26 16:04:16.570][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-07-26 16:04:16.572][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-07-26 16:04:16.573][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-07-26 16:04:16.575][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-07-26 16:04:16.577][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-07-26 16:04:16.578][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-07-26 16:04:16.580][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-07-26 16:04:16.581][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-07-26 16:04:16.583][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-07-26 16:04:16.584][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-07-26 16:04:16.586][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-07-26 16:04:16.587][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-07-26 16:04:16.589][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-07-26 16:04:16.591][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-07-26 16:04:16.592][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-07-26 16:04:16.594][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-07-26 16:04:16.595][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-07-26 16:04:16.597][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-07-26 16:04:16.599][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-07-26 16:04:16.600][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-07-26 16:04:16.602][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-07-26 16:04:16.603][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-07-26 16:04:16.605][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-07-26 16:04:16.606][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-07-26 16:04:16.608][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-07-26 16:04:16.610][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-07-26 16:04:16.611][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-07-26 16:04:16.613][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-07-26 16:04:16.614][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-07-26 16:04:16.616][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-07-26 16:04:16.617][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-07-26 16:04:16.619][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-07-26 16:04:16.620][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-07-26 16:04:16.622][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-07-26 16:04:16.624][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-07-26 16:04:16.625][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-07-26 16:04:16.627][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-07-26 16:04:16.628][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-07-26 16:04:16.630][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-07-26 16:04:16.631][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-07-26 16:04:16.633][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-07-26 16:04:16.635][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-07-26 16:04:16.637][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-07-26 16:04:16.638][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-26 16:04:16.639][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.642][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.732][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[2025-07-26 16:04:16.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.756][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.DEBUG[2025-07-26 16:04:16.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:16.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:16.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:16.782][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-07-26 16:04:16.785][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-07-26 16:04:16.787][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.788][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-07-26 16:04:16.789][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.790][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:16.791][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.793][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.794][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.795][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.796][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-07-26 16:04:16.797][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:16.799][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.800][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-07-26 16:04:16.801][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:16.802][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-07-26 16:04:16.802][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-07-26 16:04:16.804][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.805][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.806][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-07-26 16:04:16.807][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.808][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.810][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:16.811][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.812][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.813][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.814][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-07-26 16:04:16.814][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-07-26 16:04:16.815][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:16.817][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:16.818][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.819][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.820][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-07-26 16:04:16.822][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.824][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-07-26 16:04:16.825][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.826][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:16.827][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.828][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.830][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.831][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.832][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-07-26 16:04:16.833][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:16.834][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.836][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-07-26 16:04:16.837][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:16.838][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-07-26 16:04:16.838][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-07-26 16:04:16.838][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-07-26 16:04:16.838][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-07-26 16:04:16.838][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-07-26 16:04:16.838][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-07-26 16:04:16.839][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.840][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:04:16.842][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-07-26 16:04:16.843][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.844][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.845][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:16.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.848][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.850][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-07-26 16:04:16.850][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-07-26 16:04:16.851][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:16.852][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:16.853][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.854][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.856][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-07-26 16:04:16.858][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.859][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-07-26 16:04:16.860][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.861][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:16.863][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.864][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.865][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.866][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.867][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-07-26 16:04:16.869][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:16.870][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.871][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-07-26 16:04:16.872][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:16.873][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-07-26 16:04:16.873][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:16.873][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:16.873][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:16.873][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:16.873][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:16.873][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:16.873][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:16.873][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:16.873][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:16.873][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-07-26 16:04:16.873][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:16.873][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:16.873][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:16.875][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.876][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:04:16.876][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-26 16:04:16.876][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-26 16:04:16.877][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-07-26 16:04:16.878][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.880][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.881][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:16.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.884][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.885][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-07-26 16:04:16.885][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-07-26 16:04:16.885][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-07-26 16:04:16.887][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:16.888][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:16.889][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.890][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-07-26 16:04:16.891][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-07-26 16:04:16.893][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.895][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-07-26 16:04:16.896][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.897][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:16.898][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.899][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.901][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.902][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.903][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-07-26 16:04:16.904][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:16.905][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.907][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-07-26 16:04:16.908][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:16.909][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-07-26 16:04:16.909][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-07-26 16:04:16.910][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:16.911][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:16.913][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-07-26 16:04:16.914][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.915][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.916][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:16.917][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:16.918][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:16.919][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:16.921][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-07-26 16:04:16.921][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-07-26 16:04:16.921][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-07-26 16:04:16.922][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:16.923][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:16.924][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:16.925][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-07-26 16:04:16.927][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-07-26 16:04:16.928][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-07-26 16:04:16.930][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-07-26 16:04:16.932][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-07-26 16:04:16.934][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-07-26 16:04:16.935][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-07-26 16:04:16.950][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2025-07-26 16:04:16.951][super$initialize] Register connector ncbi.pubchem.comp with the request scheduler
biodb.DEBUG[2025-07-26 16:04:16.952][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.pubchem.comp.
biodb.DEBUG[2025-07-26 16:04:16.954][private$addConnectorRules] Create new rule for URL "pubchem.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.comp".
biodb.DEBUG[2025-07-26 16:04:16.956][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-07-26 16:04:16.957][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-07-26 16:04:16.959][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.comp".
biodb.DEBUG[2025-07-26 16:04:16.960][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-07-26 16:04:16.961][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-07-26 16:04:16.963][rule$addConnector] Connector "ncbi.pubchem.comp" is already listed in rule "pubchem.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-07-26 16:04:16.968][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2025-07-26 16:04:16.973][biodb::testThat]
biodb.INFO [2025-07-26 16:04:16.974][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-07-26 16:04:16.975][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:16.976][biodb::testThat]
biodb.TRACE[2025-07-26 16:04:16.981][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2025-07-26 16:04:16.982][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:04:16.986][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-07-26 16:04:16.987][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:16.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:16.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:16.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:16.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:16.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:17.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:17.005][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.006][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.008][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.015][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.016][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.018][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.020][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.025][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.026][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.029][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.030][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.035][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.037][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.039][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.041][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.046][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.047][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.049][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.051][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.056][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.057][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.060][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.061][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.066][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:17.067][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:17.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.070][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.071][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:17.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:17.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.076][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:17.077][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:17.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.080][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.081][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:17.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:17.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.086][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:17.088][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:17.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.090][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.091][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:17.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:17.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.096][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.098][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.100][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.107][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:17.108][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:17.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.110][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.112][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:17.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:17.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.117][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:17.118][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:17.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.120][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:17.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:17.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.127][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:17.128][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:17.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.130][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.132][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:17.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:17.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.137][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:17.138][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:17.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.140][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.142][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:17.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:17.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.147][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-07-26 16:04:17.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.152][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.157][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.161][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-07-26 16:04:17.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.166][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.171][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.176][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-07-26 16:04:17.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.181][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.185][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.190][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-07-26 16:04:17.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.195][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.200][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.205][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-07-26 16:04:17.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.209][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.214][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.219][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:17.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:17.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.224][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:17.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:17.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.229][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:17.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:17.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.238][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:17.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:17.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:17.272][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2025-07-26 16:04:17.275][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:17.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:17.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.279][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:17.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:17.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.284][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:17.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:17.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.289][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:17.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:17.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.294][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:17.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:17.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.299][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:17.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:17.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.304][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:17.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:17.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.321][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:17.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:17.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.362][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:17.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:17.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.367][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:17.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:17.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.372][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:17.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:17.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.400][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.401][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.403][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.426][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:17.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:17.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:17.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:17.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:17.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:17.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.440][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:17.442][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:17.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.444][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.445][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:17.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:17.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:17.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:17.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:17.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:17.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:17.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:17.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.474][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:17.475][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:17.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.478][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:17.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:17.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.494][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:17.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:17.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.499][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:17.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:17.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.503][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:17.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:17.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.508][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:17.510][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:17.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.512][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.513][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:17.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:17.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.528][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:17.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:17.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.533][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:17.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:17.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.538][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:17.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:17.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.543][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:17.544][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:17.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.547][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.548][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:17.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:17.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.562][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:17.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:17.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.568][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:17.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:17.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.572][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:17.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:17.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.577][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:17.579][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:17.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.581][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.582][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:17.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:17.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.597][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:17.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:17.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.602][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:17.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:17.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.607][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:17.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:17.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.612][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:17.613][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:17.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.615][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.616][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:17.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:17.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.631][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.636][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.641][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.646][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.647][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.650][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.651][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.665][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.670][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.675][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.680][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.681][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.684][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.685][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.699][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.704][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.709][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.714][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.715][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.718][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.719][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.735][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.740][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.745][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.749][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.751][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.753][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.754][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.769][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.774][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.779][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.784][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.785][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.787][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.788][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:17.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:17.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:17.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:17.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:17.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:17.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.817][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:17.819][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:17.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.821][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:17.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:17.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.837][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.842][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.851][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.853][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.855][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:17.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:17.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.876][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:17.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:17.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:17.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:17.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.892][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:17.893][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:17.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.895][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:17.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:17.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.911][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:17.913][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:17.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.915][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.922][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.924][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:17.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.926][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.933][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.934][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:17.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.937][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.943][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.945][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:17.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.947][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.954][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.956][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:17.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.958][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.965][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.966][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:17.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.968][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.975][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:17.977][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:17.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.979][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.986][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:17.987][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:17.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:17.989][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:17.996][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.998][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:17.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.000][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.007][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:18.008][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:18.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.011][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.017][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:18.019][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:18.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.021][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.028][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:18.029][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:18.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.032][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.039][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:18.040][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:18.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.042][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.049][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.050][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.053][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.060][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.061][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.063][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.072][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2025-07-26 16:04:18.074][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:04:18.075][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-07-26 16:04:18.077][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:18.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:18.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:18.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:18.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:18.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:18.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:18.093][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.094][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.097][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.103][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.104][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.107][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.108][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.113][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.115][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.117][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.119][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.124][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.125][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.127][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.129][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.134][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.135][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.137][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.139][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.144][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.145][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.148][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.150][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.155][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:18.156][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:18.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.158][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.160][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:18.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:18.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.165][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:18.166][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:18.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.169][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.170][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:18.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:18.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.175][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:18.176][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:18.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.179][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.180][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:18.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:18.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.185][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:18.186][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:18.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.189][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.190][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:18.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:18.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.195][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:18.197][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:18.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.199][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.200][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:18.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:18.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.205][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:18.207][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:18.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.209][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.211][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:18.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:18.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.216][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.217][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.219][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.221][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.226][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.227][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.229][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.231][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.236][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-07-26 16:04:18.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.241][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.246][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.250][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-07-26 16:04:18.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.255][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.260][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.265][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-07-26 16:04:18.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.270][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.275][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.279][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-07-26 16:04:18.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.284][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.289][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.294][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-07-26 16:04:18.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.299][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.304][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.309][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:18.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:18.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.314][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:18.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:18.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.319][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:18.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:18.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.328][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:18.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:18.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:18.362][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2025-07-26 16:04:18.365][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:18.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:18.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.370][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:18.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:18.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.381][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:18.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:18.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.386][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:18.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:18.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.391][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:18.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:18.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.395][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:18.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:18.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.400][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:18.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:18.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.417][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:18.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:18.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.459][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:18.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:18.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.464][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:18.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:18.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.468][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:18.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:18.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.496][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.497][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.500][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:18.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:18.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:18.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:18.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:18.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:18.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:18.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:18.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.530][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:18.532][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:18.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.534][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:18.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:18.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:18.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:18.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:18.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:18.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:18.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:18.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.564][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:18.566][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:18.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.568][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:18.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:18.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.584][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:18.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:18.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.588][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:18.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:18.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.593][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:18.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:18.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.598][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:18.599][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:18.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.602][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.603][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:18.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:18.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.617][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:18.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:18.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.622][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:18.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:18.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.627][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:18.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:18.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.632][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:18.633][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:18.634][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.635][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.637][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:18.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:18.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.651][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.656][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.661][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.666][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.667][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.670][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.671][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:18.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.685][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.691][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.695][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.700][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.701][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.704][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.705][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:18.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.720][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:18.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:18.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.725][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:18.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:18.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:18.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:18.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.736][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:18.738][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:18.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.741][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:18.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:18.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:18.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:18.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.762][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:18.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:18.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.767][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:18.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:18.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.772][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:18.773][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:18.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.775][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:18.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:18.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.791][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.796][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.801][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.806][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.807][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.810][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.811][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:18.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.826][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.831][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.835][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.840][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.842][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.844][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.845][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:18.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.866][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.871][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.876][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.880][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.882][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.883][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.884][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.885][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:18.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.900][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.905][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.910][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.914][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.916][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.918][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.919][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:18.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.934][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.939][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.944][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.949][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.950][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.952][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.953][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:18.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:18.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:18.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.973][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:18.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:18.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.978][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:18.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:18.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.983][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:18.984][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:18.985][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.986][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:18.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:18.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:18.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:18.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.002][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.004][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.006][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.013][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.014][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.016][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.023][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.024][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.027][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.033][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.035][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.037][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.044][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.045][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.047][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.054][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.055][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.058][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.064][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:19.066][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:19.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.068][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.075][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:19.076][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:19.077][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.078][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.085][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:19.086][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:19.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.089][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.095][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:19.096][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:19.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.099][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.105][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:19.107][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:19.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.109][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.116][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:19.117][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:19.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.119][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.126][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:19.127][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:19.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.129][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.136][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:19.137][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:19.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.140][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.146][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:19.147][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:19.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.150][ef$get] fields variable is a list.
biodb.INFO [2025-07-26 16:04:19.162][biodb::testThat]
biodb.INFO [2025-07-26 16:04:19.163][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-07-26 16:04:19.164][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:19.165][biodb::testThat]
biodb.DEBUG[2025-07-26 16:04:19.168][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-07-26 16:04:19.170][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
biodb.TRACE[2025-07-26 16:04:19.173][cch$loadFileContent] Trying to load 2 files from cache: [2]: "2, 65124".
biodb.TRACE[2025-07-26 16:04:19.176][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-07-26 16:04:19.202][loadFileContents] Loaded 2 files from cache: [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/2.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/65124.xml".
biodb.DEBUG[2025-07-26 16:04:19.203][conn$getEntryContent] 2 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-07-26 16:04:19.205][self$createEntryFromContent] Creating PubChem Compound entries from 2 content(s).
biodb.DEBUG[2025-07-26 16:04:19.207][self$createEntryFromContent] Parsing 2 PubChem Compound entries.
biodb.DEBUG[2025-07-26 16:04:19.208][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:19.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:19.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:19.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:19.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:19.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:19.221][FUN] Functions in observer BiodbConfig: [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[2025-07-26 16:04:19.224][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.225][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.227][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.234][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.235][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.237][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.239][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.244][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.245][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.248][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.249][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.254][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.255][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.258][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.259][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.264][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.265][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.268][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.269][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.274][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.275][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.278][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.279][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.284][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:19.286][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:19.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.288][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.289][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:19.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:19.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.294][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:19.296][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:19.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.298][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.299][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:19.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:19.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.304][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:19.306][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:19.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.308][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.309][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:19.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:19.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.314][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:19.316][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:19.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.318][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.319][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:19.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:19.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.324][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:19.326][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:19.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.328][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.329][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:19.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:19.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.334][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:19.336][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:19.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.338][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:19.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:19.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.344][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:19.346][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:19.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.348][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.349][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:19.351][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:19.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.353][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.354][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-07-26 16:04:19.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.365][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.370][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.375][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-07-26 16:04:19.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.380][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.384][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.389][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-07-26 16:04:19.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.394][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.399][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.403][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-07-26 16:04:19.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.408][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.413][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.418][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-07-26 16:04:19.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.423][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.427][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.432][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:19.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:19.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.437][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:19.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:19.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.442][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:19.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:19.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.452][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:19.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:19.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:19.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:19.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:19.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:19.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:19.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:19.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:19.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:19.487][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.488][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.491][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.497][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.498][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.501][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.502][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.507][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.509][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.511][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.513][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.518][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.519][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.521][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.523][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.528][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.529][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.531][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.533][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.538][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.539][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.541][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.543][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.548][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:19.549][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:19.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.552][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.553][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:19.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:19.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.558][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:19.559][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:19.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.562][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.563][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:19.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:19.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.568][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:19.569][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:19.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.572][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:19.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:19.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.578][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:19.580][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:19.581][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.582][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:19.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:19.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.588][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:19.590][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:19.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.592][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.594][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:19.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:19.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.599][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:19.600][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:19.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.602][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:19.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:19.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.609][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:19.610][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:19.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.612][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.614][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:19.615][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:19.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.617][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.619][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-07-26 16:04:19.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.624][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.628][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:19.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.633][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-07-26 16:04:19.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.638][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.643][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:19.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.648][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-07-26 16:04:19.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.652][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.657][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:19.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.662][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-07-26 16:04:19.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.667][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.672][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:19.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.676][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-07-26 16:04:19.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.681][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.686][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:19.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:19.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:19.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.696][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:19.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:19.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.701][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:19.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:19.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.710][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:19.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:19.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:19.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:19.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:19.771][self$createEntryFromContent] Accession numbers: 2, 65124.
biodb.TRACE[2025-07-26 16:04:19.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-07-26 16:04:19.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-07-26 16:04:19.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-07-26 16:04:19.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-07-26 16:04:19.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-07-26 16:04:19.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-07-26 16:04:19.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-07-26 16:04:19.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-07-26 16:04:19.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-07-26 16:04:19.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-07-26 16:04:19.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-07-26 16:04:19.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-07-26 16:04:19.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-07-26 16:04:19.818][biodb::testThat]
biodb.INFO [2025-07-26 16:04:19.820][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-07-26 16:04:19.821][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:19.822][biodb::testThat]
biodb.TRACE[2025-07-26 16:04:19.826][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:19.827][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:19.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.829][ef$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:19.831][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.TRACE[2025-07-26 16:04:19.854][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:19.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:19.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.859][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:19.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:19.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.864][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:19.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:19.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:19.872][function(conn, opt)] With value "(2-acetyloxy-3-carboxypropyl)-trimethylazanium".
biodb.DEBUG[2025-07-26 16:04:19.878][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term="(2-acetyloxy-3-carboxypropyl)-trimethylazanium"[IUPACName]&retmax=10".
biodb.DEBUG[2025-07-26 16:04:19.882][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:19.883][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0c7e343368bb974cc0f019187ff4a141".
biodb.TRACE[2025-07-26 16:04:19.885][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:19.899][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/0c7e343368bb974cc0f019187ff4a141.content".
biodb.DEBUG[2025-07-26 16:04:19.902][function(conn, opt)] With found IDs [5]: "87229113, 25217148, 450343, 450342, 2".
biodb.TRACE[2025-07-26 16:04:19.920][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:19.921][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:19.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.924][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.925][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:19.926][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:19.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.929][ef$get] fields variable is a list.
biodb.INFO [2025-07-26 16:04:19.935][biodb::testThat]
biodb.INFO [2025-07-26 16:04:19.937][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-07-26 16:04:19.938][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:19.939][biodb::testThat]
biodb.TRACE[2025-07-26 16:04:19.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:19.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:19.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.972][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:19.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:19.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:19.977][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:19.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:19.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:19.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:20.022][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term="(2-acetyloxy-3-carboxypropyl)-trimethylazanium"[IUPACName]&retmax=10".
biodb.DEBUG[2025-07-26 16:04:20.026][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:20.028][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0c7e343368bb974cc0f019187ff4a141".
biodb.TRACE[2025-07-26 16:04:20.029][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:20.032][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/0c7e343368bb974cc0f019187ff4a141.content".
biodb.INFO [2025-07-26 16:04:20.056][biodb::testThat]
biodb.INFO [2025-07-26 16:04:20.057][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-07-26 16:04:20.059][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:20.060][biodb::testThat]
biodb.TRACE[2025-07-26 16:04:20.072][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:20.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:20.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.078][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:20.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:20.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.083][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:20.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:20.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.087][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:20.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:20.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.092][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:20.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:20.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.097][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:20.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:20.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.102][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:20.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:20.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.109][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:20.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:20.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.114][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:20.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:20.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.119][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:20.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:20.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.123][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:20.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:20.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.128][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:20.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:20.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.133][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:20.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:20.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.138][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:20.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:20.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-07-26 16:04:20.151][biodb::testThat]
biodb.INFO [2025-07-26 16:04:20.153][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-07-26 16:04:20.154][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:20.155][biodb::testThat]
biodb.INFO [2025-07-26 16:04:20.167][biodb::testThat]
biodb.INFO [2025-07-26 16:04:20.168][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-07-26 16:04:20.169][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:20.171][biodb::testThat]
biodb.INFO [2025-07-26 16:04:20.183][biodb::testThat]
biodb.INFO [2025-07-26 16:04:20.184][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-07-26 16:04:20.185][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:20.186][biodb::testThat]
biodb.DEBUG[2025-07-26 16:04:20.191][function(conn, opt)] Trying to download "https://pubchem.ncbi.nlm.nih.gov/compound/2".
biodb.DEBUG[2025-07-26 16:04:20.341][getUrlContent] Use RCurl for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/compound/2.
biodb.INFO [2025-07-26 16:04:20.434][biodb::testThat]
biodb.INFO [2025-07-26 16:04:20.436][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-07-26 16:04:20.437][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:20.438][biodb::testThat]
biodb.DEBUG[2025-07-26 16:04:20.573][getUrlContent] Use RCurl for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=2&t=l.
biodb.TRACE[2025-07-26 16:04:20.649][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:20.651][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:20.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.653][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.655][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:20.656][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:20.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.658][ef$get] fields variable is a list.
biodb.INFO [2025-07-26 16:04:20.661][biodb::testThat]
biodb.INFO [2025-07-26 16:04:20.662][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-07-26 16:04:20.663][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:20.665][biodb::testThat]
biodb.TRACE[2025-07-26 16:04:20.680][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:20.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:20.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.686][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:20.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:20.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:20.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:20.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:20.795][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term="(2-acetyloxy-3-carboxypropyl)-trimethylazanium"[IUPACName]&retmax=10".
biodb.DEBUG[2025-07-26 16:04:20.799][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:20.801][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0c7e343368bb974cc0f019187ff4a141".
biodb.TRACE[2025-07-26 16:04:20.803][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:20.805][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/0c7e343368bb974cc0f019187ff4a141.content".
biodb.DEBUG[2025-07-26 16:04:20.880][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term="(2-acetyloxy-3-carboxypropyl)-trimethylazanium"[IUPACName]&retmax=10".
biodb.DEBUG[2025-07-26 16:04:20.884][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:20.886][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0c7e343368bb974cc0f019187ff4a141".
biodb.TRACE[2025-07-26 16:04:20.888][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:20.890][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/0c7e343368bb974cc0f019187ff4a141.content".
biodb.TRACE[2025-07-26 16:04:20.910][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-26 16:04:20.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-26 16:04:20.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:20.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:20.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:20.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:20.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:20.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:20.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:20.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:20.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:20.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:20.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:20.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:20.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:20.955][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.23:204.25[MolecularWeight]&retmax=3".
biodb.DEBUG[2025-07-26 16:04:20.959][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:20.960][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2616ca37a6f6e1bc281f8c51bc53ce81".
biodb.TRACE[2025-07-26 16:04:20.962][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:20.977][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/2616ca37a6f6e1bc281f8c51bc53ce81.content".
biodb.DEBUG[2025-07-26 16:04:20.997][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.23:204.25[MolecularWeight]&retmax=1000000".
biodb.DEBUG[2025-07-26 16:04:21.001][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:21.003][cch$loadFileContent] Trying to load 1 files from cache: [1]: "43af01c58cfaf2fe3448c11004a21986".
biodb.TRACE[2025-07-26 16:04:21.005][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:21.032][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/43af01c58cfaf2fe3448c11004a21986.content".
biodb.DEBUG[2025-07-26 16:04:21.333][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term="(2-acetyloxy-3-carboxypropyl)-trimethylazanium"[IUPACName] AND 204.23:204.25[MolecularWeight]&retmax=1000000".
biodb.DEBUG[2025-07-26 16:04:21.337][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:21.339][cch$loadFileContent] Trying to load 1 files from cache: [1]: "5a651e56a091cb06291b388106735d55".
biodb.TRACE[2025-07-26 16:04:21.341][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:21.356][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/5a651e56a091cb06291b388106735d55.content".
biodb.DEBUG[2025-07-26 16:04:21.387][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term="(2-acetyloxy-3-carboxypropyl)-trimethylazanium"[IUPACName] AND 204.23:204.27[MolecularWeight]&retmax=1000000".
biodb.DEBUG[2025-07-26 16:04:21.391][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:21.393][cch$loadFileContent] Trying to load 1 files from cache: [1]: "d3d0da2755d093596dae584b7698bc73".
biodb.TRACE[2025-07-26 16:04:21.395][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:21.415][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/d3d0da2755d093596dae584b7698bc73.content".
biodb.TRACE[2025-07-26 16:04:21.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:21.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:21.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:21.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:21.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:21.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:21.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:21.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:21.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:21.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:21.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:21.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:21.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:21.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:21.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:21.676][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.12358305:204.12358307[MonoisotopicMass]&retmax=3".
biodb.DEBUG[2025-07-26 16:04:21.680][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:21.682][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1384af38a786fc6768cd7f1e796d96ab".
biodb.TRACE[2025-07-26 16:04:21.683][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:21.699][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/1384af38a786fc6768cd7f1e796d96ab.content".
biodb.DEBUG[2025-07-26 16:04:21.719][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.12358305:204.12358307[MonoisotopicMass]&retmax=1000000".
biodb.DEBUG[2025-07-26 16:04:21.724][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:21.727][cch$loadFileContent] Trying to load 1 files from cache: [1]: "983d3a3af3901d23b5d919d379c6bd32".
biodb.TRACE[2025-07-26 16:04:21.729][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:21.747][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/983d3a3af3901d23b5d919d379c6bd32.content".
biodb.DEBUG[2025-07-26 16:04:21.769][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term="(2-acetyloxy-3-carboxypropyl)-trimethylazanium"[IUPACName] AND 204.12358305:204.12358307[MonoisotopicMass]&retmax=1000000".
biodb.DEBUG[2025-07-26 16:04:21.773][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:21.774][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9a9be2efcff8c77fef3b8a87f25b444".
biodb.TRACE[2025-07-26 16:04:21.776][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:21.792][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/b9a9be2efcff8c77fef3b8a87f25b444.content".
biodb.DEBUG[2025-07-26 16:04:21.822][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term="(2-acetyloxy-3-carboxypropyl)-trimethylazanium"[IUPACName] AND 204.12358305:204.12358309[MonoisotopicMass]&retmax=1000000".
biodb.DEBUG[2025-07-26 16:04:21.826][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:21.827][cch$loadFileContent] Trying to load 1 files from cache: [1]: "6d4e46c6f0a021fc6e92911d60537192".
biodb.TRACE[2025-07-26 16:04:21.829][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:21.833][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/6d4e46c6f0a021fc6e92911d60537192.content".
biodb.TRACE[2025-07-26 16:04:21.856][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-07-26 16:04:21.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-07-26 16:04:21.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-07-26 16:04:21.873][biodb::testThat]
biodb.INFO [2025-07-26 16:04:21.874][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-07-26 16:04:21.876][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:21.877][biodb::testThat]
biodb.TRACE[2025-07-26 16:04:21.881][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-26 16:04:21.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-26 16:04:21.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:21.886][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-26 16:04:21.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-26 16:04:21.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:21.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:21.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:21.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:21.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:21.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:21.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:21.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:21.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:21.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:21.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:21.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:21.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:21.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:21.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:21.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:21.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:21.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:21.952][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.23:204.25[MolecularWeight]&retmax=3".
biodb.DEBUG[2025-07-26 16:04:21.956][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:21.957][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2616ca37a6f6e1bc281f8c51bc53ce81".
biodb.TRACE[2025-07-26 16:04:21.959][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:21.962][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/2616ca37a6f6e1bc281f8c51bc53ce81.content".
biodb.DEBUG[2025-07-26 16:04:21.964][private$loadEntries] Creating entries from ids [3]: "176448968, 176448013, 176448011".
biodb.DEBUG[2025-07-26 16:04:21.965][conn$getEntryContent] Get PubChem Compound entry content(s) for 3 id(s)...
biodb.TRACE[2025-07-26 16:04:21.967][cch$loadFileContent] Trying to load 3 files from cache: [3]: "176448968, 176448013, 176448011".
biodb.TRACE[2025-07-26 16:04:21.969][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2025-07-26 16:04:22.009][loadFileContents] Loaded 3 files from cache: [3]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/176448968.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/176448013.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/176448011.xml".
biodb.DEBUG[2025-07-26 16:04:22.010][conn$getEntryContent] 3 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-07-26 16:04:22.012][self$createEntryFromContent] Creating PubChem Compound entries from 3 content(s).
biodb.DEBUG[2025-07-26 16:04:22.013][self$createEntryFromContent] Parsing 3 PubChem Compound entries.
biodb.DEBUG[2025-07-26 16:04:22.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:22.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:22.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:22.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:22.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:22.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:22.028][FUN] Functions in observer BiodbConfig: [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[2025-07-26 16:04:22.031][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.032][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.034][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.041][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:22.042][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:22.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.044][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.046][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:22.047][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:22.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.049][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.051][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:22.052][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:22.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.054][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.056][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:22.057][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:22.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.059][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.061][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:22.062][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:22.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.064][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.066][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:22.067][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:22.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.069][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.071][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:22.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:22.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.076][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:22.077][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:22.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.079][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.081][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:22.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:22.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.086][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:22.087][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:22.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.089][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.091][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:22.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:22.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.096][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:22.097][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:22.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.099][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:22.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:22.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.106][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:22.107][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:22.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.109][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.111][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:22.112][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:22.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.114][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:22.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:22.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.121][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:22.122][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:22.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.124][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.126][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:22.127][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:22.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.129][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.131][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-07-26 16:04:22.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:22.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.135][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-07-26 16:04:22.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:22.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.140][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-07-26 16:04:22.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:22.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.145][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-07-26 16:04:22.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:22.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.150][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-07-26 16:04:22.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:22.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.155][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.159][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.169][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:22.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:22.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:22.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:22.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:22.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:22.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:22.201][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[2025-07-26 16:04:22.205][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.206][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.209][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.215][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:22.217][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:22.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.219][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.220][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:22.222][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:22.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.224][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.225][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:22.227][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:22.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.229][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.231][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:22.232][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:22.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.234][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.236][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:22.242][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:22.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.245][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.246][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:22.247][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:22.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.249][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.251][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:22.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:22.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.256][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:22.257][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:22.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.260][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.261][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:22.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:22.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.266][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:22.267][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:22.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.269][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:22.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:22.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.276][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:22.277][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:22.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.279][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.281][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:22.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:22.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.286][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:22.287][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:22.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.289][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.291][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:22.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:22.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.296][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:22.297][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:22.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.299][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:22.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:22.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.306][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:22.307][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:22.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.309][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.311][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:22.312][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:22.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.314][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.316][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-07-26 16:04:22.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:22.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.321][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-07-26 16:04:22.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:22.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.325][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-07-26 16:04:22.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:22.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.330][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-07-26 16:04:22.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:22.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.335][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-07-26 16:04:22.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:22.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.339][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.344][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.354][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:22.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:22.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:22.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:22.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:22.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:22.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:22.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:22.388][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.389][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.392][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.398][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:22.399][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:22.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.402][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.403][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:22.404][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:22.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.407][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.408][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:22.409][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:22.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.412][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.413][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:22.414][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:22.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.417][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.418][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:22.419][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:22.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.422][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.423][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:22.425][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:22.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.427][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.428][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:22.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:22.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.433][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:22.435][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:22.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.437][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.438][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:22.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:22.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.443][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:22.444][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:22.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.447][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.448][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:22.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:22.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.453][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:22.454][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:22.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.457][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.458][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:22.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:22.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.463][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:22.464][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:22.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.467][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.468][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:22.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:22.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.473][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:22.474][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:22.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.477][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:22.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:22.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.483][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:22.484][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:22.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.487][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.488][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:22.489][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:22.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.492][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.493][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-07-26 16:04:22.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:22.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.498][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-07-26 16:04:22.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:22.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.503][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-07-26 16:04:22.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:22.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.507][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-07-26 16:04:22.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:22.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.512][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-07-26 16:04:22.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:22.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.517][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.522][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.531][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:22.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:22.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:22.593][self$createEntryFromContent] Accession numbers: 176448968, 176448013, 176448011.
biodb.DEBUG[2025-07-26 16:04:22.595][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-07-26 16:04:22.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:22.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:22.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:22.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:22.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:22.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:22.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:22.611][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.615][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.620][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:22.621][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-07-26 16:04:22.623][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-07-26 16:04:22.624][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-07-26 16:04:22.625][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:22.626][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.627][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.630][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.631][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.632][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.635][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.636][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:22.637][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:22.638][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.639][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.642][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.643][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-07-26 16:04:22.644][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.649][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.654][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.667][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [176448968].
biodb.DEBUG[2025-07-26 16:04:22.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:22.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:22.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:22.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:22.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:22.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:22.681][FUN] Functions in observer BiodbConfig: [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[2025-07-26 16:04:22.682][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.687][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.697][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:22.699][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-07-26 16:04:22.700][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-07-26 16:04:22.701][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-07-26 16:04:22.702][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:22.703][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.704][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.707][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.708][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.709][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.712][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.713][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:22.714][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:22.715][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.716][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.719][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.720][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-07-26 16:04:22.721][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.726][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.731][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.736][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [176448013].
biodb.DEBUG[2025-07-26 16:04:22.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:22.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:22.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:22.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:22.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:22.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:22.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:22.753][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.758][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.763][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:22.764][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-07-26 16:04:22.765][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-07-26 16:04:22.766][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-07-26 16:04:22.767][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:22.768][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.770][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.772][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.773][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.774][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.777][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.778][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:22.779][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:22.780][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.782][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.784][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.785][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-07-26 16:04:22.786][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.791][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.796][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:22.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:22.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:22.801][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [176448011].
biodb.DEBUG[2025-07-26 16:04:22.802][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-07-26 16:04:22.803][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.DEBUG[2025-07-26 16:04:22.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:22.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:22.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:22.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:22.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:22.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:22.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:22.826][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18:226.2[MolecularWeight]&retmax=3".
biodb.DEBUG[2025-07-26 16:04:22.830][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:22.831][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:22.833][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:22.964][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:23.036][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:23.037][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:23.038][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:23.040][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:23.164][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:23.234][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:23.235][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:23.237][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:23.238][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:23.356][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:23.421][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:23.422][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:23.423][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:23.425][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:23.548][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:23.619][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:23.621][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:23.622][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:23.624][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:23.751][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:23.816][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:23.818][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:23.819][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:23.821][rule$waitAsNeeded] Wait 0.0116429 second(s).
biodb.TRACE[2025-07-26 16:04:23.850][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:23.977][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:24.049][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:24.051][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:24.052][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:24.054][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:24.182][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:24.247][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:24.249][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:24.250][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:24.252][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:24.379][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:24.458][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:24.459][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:24.461][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:24.463][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:24.606][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:24.671][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:24.672][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:24.674][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:24.676][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:24.808][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:24.882][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.INFO [2025-07-26 16:04:24.897][biodb::testThat]
biodb.INFO [2025-07-26 16:04:24.899][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-07-26 16:04:24.900][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:24.901][biodb::testThat]
biodb.TRACE[2025-07-26 16:04:24.905][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-26 16:04:24.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-26 16:04:24.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:24.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:24.910][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-26 16:04:24.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-26 16:04:24.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:24.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:24.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:24.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:24.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:24.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:24.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:24.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:24.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:24.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:24.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:24.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:24.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:24.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:24.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:24.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:24.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:24.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:24.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:24.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:24.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:25.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:25.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:25.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:25.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:25.011][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[2025-07-26 16:04:25.018][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.2369364:204.2430636[MolecularWeight]&retmax=3".
biodb.DEBUG[2025-07-26 16:04:25.021][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:25.023][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aa9cb23a1eb4b2596e7c242b1c35f744".
biodb.TRACE[2025-07-26 16:04:25.025][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:25.040][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/aa9cb23a1eb4b2596e7c242b1c35f744.content".
biodb.DEBUG[2025-07-26 16:04:25.042][private$loadEntries] Creating entries from ids [3]: "176438704, 176415432, 176414946".
biodb.DEBUG[2025-07-26 16:04:25.043][conn$getEntryContent] Get PubChem Compound entry content(s) for 3 id(s)...
biodb.TRACE[2025-07-26 16:04:25.045][cch$loadFileContent] Trying to load 3 files from cache: [3]: "176438704, 176415432, 176414946".
biodb.TRACE[2025-07-26 16:04:25.047][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2025-07-26 16:04:25.089][loadFileContents] Loaded 3 files from cache: [3]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/176438704.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/176415432.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/176414946.xml".
biodb.DEBUG[2025-07-26 16:04:25.090][conn$getEntryContent] 3 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-07-26 16:04:25.092][self$createEntryFromContent] Creating PubChem Compound entries from 3 content(s).
biodb.DEBUG[2025-07-26 16:04:25.094][self$createEntryFromContent] Parsing 3 PubChem Compound entries.
biodb.DEBUG[2025-07-26 16:04:25.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:25.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:25.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:25.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:25.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:25.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:25.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:25.111][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.113][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.129][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.136][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.137][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.139][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.141][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.146][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.147][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.149][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.151][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.156][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.157][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.159][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.161][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.166][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.167][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.169][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.171][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.176][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.177][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.179][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.181][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.186][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:25.187][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:25.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.189][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.191][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:25.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:25.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.196][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:25.197][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:25.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.199][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.201][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:25.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:25.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.205][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:25.207][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:25.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.209][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.211][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:25.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:25.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.215][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:25.217][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:25.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.219][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.220][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:25.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:25.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.225][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:25.226][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:25.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.229][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.230][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:25.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:25.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.235][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:25.236][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:25.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.239][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:25.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:25.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.245][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:25.246][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:25.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.248][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.250][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:25.251][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:25.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.253][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.255][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-07-26 16:04:25.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.260][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.264][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.269][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-07-26 16:04:25.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.274][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.279][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.284][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-07-26 16:04:25.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.288][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.293][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.298][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-07-26 16:04:25.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.303][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.308][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.312][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-07-26 16:04:25.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.317][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.322][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.326][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:25.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:25.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.331][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.336][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.346][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:25.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:25.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:25.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:25.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:25.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:25.376][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:25.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:25.380][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.381][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.384][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.390][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.391][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.394][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.395][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.400][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.401][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.404][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.405][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.410][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.411][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.414][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.415][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.420][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.421][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.423][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.425][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.430][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.431][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.433][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.435][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.440][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:25.441][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:25.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.443][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.445][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:25.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:25.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.450][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:25.451][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:25.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.453][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.455][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:25.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:25.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.460][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:25.461][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:25.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.463][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.465][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:25.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:25.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.469][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:25.471][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:25.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.473][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.475][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:25.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:25.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.479][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:25.481][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:25.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.483][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.484][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:25.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:25.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.489][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:25.490][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:25.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.493][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:25.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:25.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.499][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:25.500][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:25.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.503][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.504][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:25.505][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:25.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.508][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.509][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-07-26 16:04:25.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.514][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.519][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.523][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-07-26 16:04:25.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.528][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.533][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.538][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-07-26 16:04:25.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.543][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.548][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.553][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-07-26 16:04:25.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.557][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.562][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.567][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-07-26 16:04:25.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.572][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.582][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:25.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:25.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.591][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.596][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.606][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:25.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:25.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:25.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:25.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:25.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:25.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:25.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:25.640][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.641][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.644][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.650][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.651][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.653][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.655][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.660][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.661][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.663][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.665][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.670][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.671][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.673][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.675][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.679][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.681][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.683][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.684][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.689][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.690][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.693][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.694][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.699][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:25.700][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:25.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.702][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.704][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-07-26 16:04:25.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:25.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.709][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:25.710][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:25.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.712][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.714][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:25.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:25.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.719][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:25.720][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:25.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.722][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:25.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:25.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.729][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:25.731][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:25.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.733][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:25.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:25.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.739][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:25.740][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:25.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.743][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.744][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:25.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:25.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.749][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:25.750][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:25.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.753][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-07-26 16:04:25.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:25.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.759][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:25.760][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-07-26 16:04:25.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.762][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.764][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:25.765][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-07-26 16:04:25.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.767][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.769][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-07-26 16:04:25.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.774][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.778][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:25.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.783][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-07-26 16:04:25.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.788][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.793][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:25.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.797][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-07-26 16:04:25.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.802][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.807][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:25.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.812][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-07-26 16:04:25.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.816][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.821][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:25.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.826][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-07-26 16:04:25.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.830][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.835][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:25.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:25.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:25.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.845][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.849][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.859][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:25.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:25.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:25.920][self$createEntryFromContent] Accession numbers: 176438704, 176415432, 176414946.
biodb.DEBUG[2025-07-26 16:04:25.940][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-07-26 16:04:25.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:25.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:25.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:25.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:25.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:25.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:25.973][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.TRACE[2025-07-26 16:04:25.974][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.979][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.984][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:25.985][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-07-26 16:04:25.986][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-07-26 16:04:25.987][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-07-26 16:04:25.988][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:25.990][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.996][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:25.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:25.998][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:25.999][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.001][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.003][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.004][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:26.005][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:26.006][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.008][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.010][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.011][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-07-26 16:04:26.012][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.017][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.022][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.027][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [176438704].
biodb.DEBUG[2025-07-26 16:04:26.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:26.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:26.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:26.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:26.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:26.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:26.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:26.042][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.046][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.051][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:26.052][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-07-26 16:04:26.053][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-07-26 16:04:26.054][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-07-26 16:04:26.056][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:26.057][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.058][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.060][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.062][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.063][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.065][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.066][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:26.067][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:26.068][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.070][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.071][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.072][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.073][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-07-26 16:04:26.074][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.079][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.084][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.089][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [176415432].
biodb.DEBUG[2025-07-26 16:04:26.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:26.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:26.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:26.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:26.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:26.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:26.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:26.104][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.108][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.113][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:26.114][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-07-26 16:04:26.115][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-07-26 16:04:26.116][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-07-26 16:04:26.117][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:26.119][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.120][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.122][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.124][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.125][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.127][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.128][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:26.129][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:26.130][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.132][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.134][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.135][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-07-26 16:04:26.136][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.141][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.146][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:26.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:26.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:26.151][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [176414946].
biodb.DEBUG[2025-07-26 16:04:26.152][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-07-26 16:04:26.153][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.DEBUG[2025-07-26 16:04:26.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:26.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:26.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:26.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:26.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:26.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:26.167][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[2025-07-26 16:04:26.174][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715:226.19339285[MolecularWeight]&retmax=3".
biodb.DEBUG[2025-07-26 16:04:26.177][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:26.179][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:26.181][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:26.310][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:26.382][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:26.383][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:26.384][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:26.387][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:26.513][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:26.585][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:26.586][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:26.587][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:26.589][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:26.715][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:26.789][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:26.790][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:26.792][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:26.794][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:26.921][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:26.985][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:26.987][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:26.988][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:26.990][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:27.128][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:27.201][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:27.202][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:27.203][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:27.205][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:27.333][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:27.397][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:27.398][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:27.399][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:27.401][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:27.524][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:27.596][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:27.597][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:27.599][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:27.601][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:27.719][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:27.796][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:27.797][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:27.799][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:27.801][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:27.925][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:27.996][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:27.998][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:27.999][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:28.001][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:28.132][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:28.208][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.INFO [2025-07-26 16:04:28.224][biodb::testThat]
biodb.INFO [2025-07-26 16:04:28.226][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-07-26 16:04:28.227][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:28.228][biodb::testThat]
biodb.TRACE[2025-07-26 16:04:28.232][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-26 16:04:28.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-26 16:04:28.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.237][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-26 16:04:28.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-26 16:04:28.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:28.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:28.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:28.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:28.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:28.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:28.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:28.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:28.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:28.305][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.23:204.25[MolecularWeight]&retmax=3".
biodb.DEBUG[2025-07-26 16:04:28.308][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:28.310][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2616ca37a6f6e1bc281f8c51bc53ce81".
biodb.TRACE[2025-07-26 16:04:28.311][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:28.314][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/2616ca37a6f6e1bc281f8c51bc53ce81.content".
biodb.DEBUG[2025-07-26 16:04:28.316][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-07-26 16:04:28.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:28.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:28.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:28.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:28.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:28.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:28.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:28.341][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.347][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.382][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:28.384][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-07-26 16:04:28.385][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-07-26 16:04:28.386][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-07-26 16:04:28.387][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:28.388][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.390][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.392][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.393][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.394][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.397][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.398][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:28.407][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:28.408][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.409][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.411][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.413][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-07-26 16:04:28.414][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.419][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.423][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.428][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [176448968].
biodb.DEBUG[2025-07-26 16:04:28.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:28.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:28.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:28.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:28.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:28.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:28.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:28.444][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.448][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.453][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:28.454][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-07-26 16:04:28.455][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-07-26 16:04:28.457][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-07-26 16:04:28.458][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:28.459][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.460][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.462][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.464][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.465][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.467][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.468][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:28.469][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:28.471][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.472][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.474][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.475][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-07-26 16:04:28.476][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.481][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.486][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.491][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [176448013].
biodb.DEBUG[2025-07-26 16:04:28.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:28.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:28.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:28.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:28.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:28.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:28.505][FUN] Functions in observer BiodbConfig: [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[2025-07-26 16:04:28.506][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.511][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.516][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:28.517][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-07-26 16:04:28.518][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-07-26 16:04:28.519][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-07-26 16:04:28.520][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:28.521][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.523][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.525][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.526][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.527][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.530][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.531][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:28.532][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:28.533][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.534][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.537][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.538][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-07-26 16:04:28.539][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.544][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.549][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:28.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:28.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:28.554][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [176448011].
biodb.DEBUG[2025-07-26 16:04:28.555][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-07-26 16:04:28.556][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.DEBUG[2025-07-26 16:04:28.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:28.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:28.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:28.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:28.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:28.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:28.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:28.577][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18:226.2[MolecularWeight]&retmax=3".
biodb.DEBUG[2025-07-26 16:04:28.581][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:28.582][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:28.584][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:28.711][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:28.782][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:28.783][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:28.784][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:28.786][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:28.908][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:28.974][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:28.975][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:28.976][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:28.978][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:29.107][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:29.173][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:29.175][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:29.176][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:29.178][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:29.309][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:29.374][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:29.375][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:29.376][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:29.378][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:29.503][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:29.569][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:29.570][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:29.571][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:29.573][rule$waitAsNeeded] Wait 0.0112121 second(s).
biodb.TRACE[2025-07-26 16:04:29.595][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:29.717][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:29.788][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:29.789][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:29.790][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:29.792][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:29.913][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:29.991][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:29.992][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:29.994][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:29.996][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:30.118][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:30.183][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:30.184][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:30.185][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:30.187][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:30.329][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:30.402][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:30.403][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:30.404][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:30.406][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:30.536][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:30.601][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.TRACE[2025-07-26 16:04:30.616][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:30.617][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:30.618][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:30.619][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:30.621][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.622][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:30.624][ef$get] fields variable is a list.
biodb.INFO [2025-07-26 16:04:30.626][biodb::testThat]
biodb.INFO [2025-07-26 16:04:30.628][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-07-26 16:04:30.629][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:30.630][biodb::testThat]
biodb.TRACE[2025-07-26 16:04:30.634][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-26 16:04:30.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-26 16:04:30.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:30.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:30.639][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-26 16:04:30.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-26 16:04:30.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:30.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:30.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:30.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:30.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:30.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:30.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:30.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:30.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:30.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:30.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:30.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:30.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:30.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:30.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:30.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:30.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:30.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:30.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:30.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:30.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:30.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:30.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:30.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:30.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:30.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:30.705][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03:204.25[MolecularWeight]&retmax=3".
biodb.DEBUG[2025-07-26 16:04:30.709][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:30.710][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:30.712][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:30.857][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:30.926][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:30.927][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:30.928][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:30.930][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:31.050][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:31.126][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:31.128][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:31.129][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:31.131][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:31.248][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:31.317][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:31.319][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:31.320][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:31.322][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:31.445][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:31.508][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:31.509][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:31.511][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:31.513][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:31.643][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:31.713][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:31.715][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:31.716][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:31.718][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:31.837][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:31.907][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:31.909][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:31.910][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:31.911][rule$waitAsNeeded] Wait 0.018635 second(s).
biodb.TRACE[2025-07-26 16:04:31.943][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:32.088][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:32.160][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:32.161][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:32.163][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:32.165][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:32.295][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:32.370][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:32.371][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:32.372][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:32.374][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:32.507][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:32.577][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:32.578][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:32.579][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:32.581][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:32.709][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:32.774][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.INFO [2025-07-26 16:04:32.789][biodb::testThat]
biodb.INFO [2025-07-26 16:04:32.791][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-07-26 16:04:32.792][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:32.793][biodb::testThat]
biodb.TRACE[2025-07-26 16:04:32.797][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-26 16:04:32.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-26 16:04:32.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.801][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-07-26 16:04:32.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-07-26 16:04:32.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:32.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:32.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:32.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:32.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:32.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:32.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:32.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:32.866][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.23:204.25[MolecularWeight]&retmax=3".
biodb.DEBUG[2025-07-26 16:04:32.870][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-07-26 16:04:32.871][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2616ca37a6f6e1bc281f8c51bc53ce81".
biodb.TRACE[2025-07-26 16:04:32.873][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:32.875][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/2616ca37a6f6e1bc281f8c51bc53ce81.content".
biodb.DEBUG[2025-07-26 16:04:32.877][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-07-26 16:04:32.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:32.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:32.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:32.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:32.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:32.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:32.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:32.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:32.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:32.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:32.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:32.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.902][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:32.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:32.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.907][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:32.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:32.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.912][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:32.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:32.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.916][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:32.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:32.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.921][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:32.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:32.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.926][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:32.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:32.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.931][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:32.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:32.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.936][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:32.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:32.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.941][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:32.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:32.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.945][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:32.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:32.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.950][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:32.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:32.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.955][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:32.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:32.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:32.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:32.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:32.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:32.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:32.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:32.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.974][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:32.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:32.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.979][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:32.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:32.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.983][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:32.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:32.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:32.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:32.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:32.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:32.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.007][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:33.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:33.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.012][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:33.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:33.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.016][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.021][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.026][private$selectFields] Fields [14]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2025-07-26 16:04:33.027][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-07-26 16:04:33.028][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-07-26 16:04:33.029][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-07-26 16:04:33.030][private$selectFields] Fields [14]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2025-07-26 16:04:33.032][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.033][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.035][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.036][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.038][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.040][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.041][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.042][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.045][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.046][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.047][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.049][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.051][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.052][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.054][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.055][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.057][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.059][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.060][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.061][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.064][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.065][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.066][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.068][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.069][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.071][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.073][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.074][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:33.075][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:33.077][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.078][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.079][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.080][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.082][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.084][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.085][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.087][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.089][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:33.090][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:33.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.092][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.093][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.094][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.097][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.098][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.099][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.102][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.103][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.104][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.106][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.107][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.109][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.111][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.112][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.114][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.129][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.131][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.132][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.134][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.135][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.137][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.139][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.140][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.141][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.144][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.145][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.146][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.148][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.149][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.151][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.153][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.154][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:33.155][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:33.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.158][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.159][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.160][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.162][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.164][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.165][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.167][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.168][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:33.169][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:33.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.172][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.173][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.174][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.176][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.178][private$selectFields] Fields [7]: "accession, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:33.179][private$organizeFieldsByGroups] Fields [7]: "accession, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:33.180][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.181][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.183][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.185][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.186][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.188][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.189][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.190][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.193][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.194][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.195][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.197][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.198][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.200][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.202][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.203][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.204][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.205][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.207][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.208][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.209][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.211][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.212][private$organizeFieldsByGroups] Groups [2]: "c("accession", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "ncbi.pubchem.comp.id"), list()"
biodb.TRACE[2025-07-26 16:04:33.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.228][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.233][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.238][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.300][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.305][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.309][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.318][private$entriesToListOfDataframes] Entry converted to data frame: [1, 7]: [accession, formula, inchi, inchikey, molecular.mass, ...] [176448968, C8H11N3NaS, InChI=1S/C8H11N3S.Na/c1-11-3-2-7-6(5-11)4-9-8(12)10-7;/h4H,2-3,5H2,1H3,(H-,9,10,12);/q-1;+1, VQFSPIPQUIREAP-UHFFFAOYSA-N, 204.25, ...].
biodb.DEBUG[2025-07-26 16:04:33.320][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:33.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:33.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:33.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:33.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:33.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:33.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:33.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.343][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.348][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.352][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.357][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.362][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.367][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.372][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.376][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.381][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.386][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.391][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.395][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.400][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.415][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.419][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:33.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:33.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.424][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:33.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:33.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.448][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:33.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:33.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:33.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:33.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.457][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.462][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.467][private$selectFields] Fields [14]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2025-07-26 16:04:33.468][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-07-26 16:04:33.469][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-07-26 16:04:33.470][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-07-26 16:04:33.471][private$selectFields] Fields [14]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2025-07-26 16:04:33.472][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.474][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.476][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.477][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.478][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.481][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.482][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.483][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.485][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.487][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.488][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.490][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.491][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.492][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.495][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.496][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.497][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.499][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.501][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.502][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.504][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.505][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.506][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.509][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.510][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.511][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.513][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.515][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:33.516][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:33.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.518][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.519][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.520][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.523][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.524][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.525][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.528][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.529][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:33.530][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:33.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.532][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.534][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.535][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.537][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.538][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.540][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.542][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.543][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.544][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.547][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.548][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.549][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.551][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.553][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.554][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.556][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.557][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.559][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.561][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.567][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.569][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.571][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.572][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.573][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.576][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.577][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.578][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.580][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.581][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.583][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.585][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.586][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:33.587][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:33.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.590][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.591][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.592][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.594][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.595][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.597][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.599][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.600][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:33.601][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:33.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.604][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.605][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.606][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.608][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.609][private$selectFields] Fields [8]: "accession, formula, inchi, inchikey, logp, molecular.mass, monoisotopic.mass, ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:33.611][private$organizeFieldsByGroups] Fields [8]: "accession, formula, inchi, inchikey, logp, molecular.mass, monoisotopic.mass, ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:33.612][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.613][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.615][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.616][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.618][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.620][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.621][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.622][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.624][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.626][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.627][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.629][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.630][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:33.631][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:33.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.634][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.635][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.636][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.638][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.639][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.641][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.643][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.644][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.645][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.647][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.649][private$organizeFieldsByGroups] Groups [2]: "c("accession", "formula", "inchi", "inchikey", "logp", "molecular.mass", "monoisotopic.mass", "ncbi.pubchem.comp.id"), list()"
biodb.TRACE[2025-07-26 16:04:33.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.664][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.669][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.674][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.683][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.688][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.693][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.698][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.703][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.707][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:33.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:33.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.712][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:33.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:33.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.717][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:33.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:33.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.751][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.756][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.761][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.769][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, formula, inchi, inchikey, logp, ...] [176448013, C13H17P, InChI=1S/C13H17P/c1-3-11-9-10-12(4-2)14(11)13-7-5-6-8-13/h7,11-12H,3-4,9-10H2,1-2H3/t11-,12-/m0/s1, HLMMGCMFWRPWDQ-RYUDHWBXSA-N, 1.3, ...].
biodb.DEBUG[2025-07-26 16:04:33.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:33.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:33.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:33.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:33.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:33.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:33.782][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.TRACE[2025-07-26 16:04:33.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.793][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.798][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.803][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.807][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.812][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.817][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.822][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.826][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.831][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.836][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.841][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.845][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.850][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.855][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.859][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.869][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:33.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:33.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.874][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:33.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:33.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:33.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:33.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:33.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:33.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.907][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.912][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.916][private$selectFields] Fields [14]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2025-07-26 16:04:33.917][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-07-26 16:04:33.919][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-07-26 16:04:33.920][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-07-26 16:04:33.921][private$selectFields] Fields [14]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2025-07-26 16:04:33.922][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.923][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.925][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.927][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.928][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.930][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.931][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.933][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:33.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.935][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.936][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.937][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:33.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.940][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.941][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.942][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:33.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.944][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.945][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.947][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:33.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.949][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.950][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:33.951][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:33.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.954][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.955][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:33.956][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:33.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.958][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.960][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.961][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:33.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.963][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.964][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:33.966][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:33.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.968][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.969][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.970][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:33.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.973][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.974][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.975][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:33.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.977][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.978][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:33.980][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:33.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.982][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.983][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.985][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:33.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.987][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.988][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:33.989][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:33.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.992][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.993][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.994][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-07-26 16:04:33.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:33.996][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:33.998][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:34.004][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-07-26 16:04:34.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.006][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.007][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:34.008][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-07-26 16:04:34.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.011][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.012][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:34.013][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-07-26 16:04:34.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.015][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.016][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:34.018][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-07-26 16:04:34.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.020][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.021][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:34.022][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:34.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.025][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.026][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:34.027][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:34.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.029][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.030][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:34.032][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:34.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.034][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.035][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:34.036][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:34.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.038][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.040][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:34.041][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:34.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.043][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.044][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:34.045][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:34.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.048][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.049][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-26 16:04:34.050][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-26 16:04:34.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.052][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.053][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:34.055][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:34.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.057][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.058][private$selectFields] Fields [8]: "accession, formula, inchi, inchikey, logp, molecular.mass, monoisotopic.mass, ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:34.059][private$organizeFieldsByGroups] Fields [8]: "accession, formula, inchi, inchikey, logp, molecular.mass, monoisotopic.mass, ncbi.pubchem.comp.id"
biodb.TRACE[2025-07-26 16:04:34.060][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:34.062][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:34.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.064][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.065][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:34.066][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:34.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.069][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.070][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:34.071][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:34.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.073][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.074][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:34.076][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:34.077][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.078][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.079][ef$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:34.080][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:34.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.083][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.084][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:34.085][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:34.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.087][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.088][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:34.090][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:34.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.092][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.093][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:34.094][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:34.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.096][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.098][private$organizeFieldsByGroups] Groups [2]: "c("accession", "formula", "inchi", "inchikey", "logp", "molecular.mass", "monoisotopic.mass", "ncbi.pubchem.comp.id"), list()"
biodb.TRACE[2025-07-26 16:04:34.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:34.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:34.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:34.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:34.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:34.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:34.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.113][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:34.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:34.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.118][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:34.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:34.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.123][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-26 16:04:34.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-26 16:04:34.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:34.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:34.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.132][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:34.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:34.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.137][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-26 16:04:34.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-26 16:04:34.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.142][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:34.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:34.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.147][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:34.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:34.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.151][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-26 16:04:34.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-26 16:04:34.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.156][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:34.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:34.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.161][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:34.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:34.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.166][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-07-26 16:04:34.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-07-26 16:04:34.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:34.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:34.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:34.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:34.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:34.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-26 16:04:34.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:34.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:34.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:34.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:34.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:34.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-07-26 16:04:34.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.199][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:34.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:34.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.204][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:34.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:34.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.209][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:34.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:34.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:34.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:34.217][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, formula, inchi, inchikey, logp, ...] [176448011, C13H17P, InChI=1S/C13H17P/c1-3-11-9-10-12(4-2)14(11)13-7-5-6-8-13/h7,11-12H,3-4,9-10H2,1-2H3/t11-,12-/m1/s1, HLMMGCMFWRPWDQ-VXGBXAGGSA-N, 1.3, ...].
biodb.DEBUG[2025-07-26 16:04:34.218][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-07-26 16:04:34.219][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.DEBUG[2025-07-26 16:04:34.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:34.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:34.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:34.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:34.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:34.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:34.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:34.241][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18:226.2[MolecularWeight]&retmax=3".
biodb.DEBUG[2025-07-26 16:04:34.245][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:34.246][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:34.248][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:34.381][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:34.445][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:34.446][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:34.447][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:34.449][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:34.565][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:34.644][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:34.645][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:34.647][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:34.649][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:34.775][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:34.845][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:34.847][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:34.848][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:34.850][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:34.969][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:35.039][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:35.040][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:35.041][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:35.043][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:35.171][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:35.255][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:35.256][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:35.258][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:35.260][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:35.384][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:35.449][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:35.451][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:35.452][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:35.454][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:35.577][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:35.646][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:35.647][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:35.649][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:35.651][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:35.769][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:35.838][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:35.840][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:35.841][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-07-26 16:04:35.842][rule$waitAsNeeded] Wait 0.00720787 second(s).
biodb.TRACE[2025-07-26 16:04:35.855][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:35.986][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:36.049][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-07-26 16:04:36.051][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-07-26 16:04:36.052][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-07-26 16:04:36.054][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-07-26 16:04:36.174][getRCurlRequestResult] Using RCurl package for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-07-26 16:04:36.245][private$doSendRequestLoop] HTTP error 302 (""). Redirect location to https://pubmed.ncbi.nlm.nih.gov/static-page/down_bethesda.html?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.INFO [2025-07-26 16:04:36.259][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-07-26 16:04:36.260][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.pubchem.comp from the request scheduler
biodb.INFO [2025-07-26 16:04:36.262][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2025-07-26 16:04:36.263][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-07-26 16:04:36.264][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.266][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.268][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-07-26 16:04:36.275][biodb::testContext]
biodb.INFO [2025-07-26 16:04:36.276][biodb::testContext] ********************************************************************************
biodb.INFO [2025-07-26 16:04:36.277][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2025-07-26 16:04:36.278][biodb::testContext] ********************************************************************************
biodb.INFO [2025-07-26 16:04:36.280][biodb::testContext]
biodb.INFO [2025-07-26 16:04:36.282][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-07-26 16:04:36.285][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-07-26 16:04:36.290][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-26 16:04:36.291][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-07-26 16:04:36.292][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-07-26 16:04:36.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.297][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-07-26 16:04:36.312][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-07-26 16:04:36.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.317][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-07-26 16:04:36.318][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-07-26 16:04:36.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.335][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[2025-07-26 16:04:36.337][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-07-26 16:04:36.338][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-07-26 16:04:36.339][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-07-26 16:04:36.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.344][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-07-26 16:04:36.345][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-07-26 16:04:36.346][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-07-26 16:04:36.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.351][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-07-26 16:04:36.352][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-07-26 16:04:36.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.356][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-07-26 16:04:36.358][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-07-26 16:04:36.359][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-07-26 16:04:36.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.362][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[2025-07-26 16:04:36.363][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-07-26 16:04:36.364][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-07-26 16:04:36.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.369][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-07-26 16:04:36.370][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-07-26 16:04:36.371][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-07-26 16:04:36.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.376][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-07-26 16:04:36.377][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-07-26 16:04:36.378][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-07-26 16:04:36.379][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-07-26 16:04:36.380][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-07-26 16:04:36.382][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-07-26 16:04:36.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.386][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-07-26 16:04:36.387][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-07-26 16:04:36.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.390][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[2025-07-26 16:04:36.392][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-07-26 16:04:36.393][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-07-26 16:04:36.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.397][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-07-26 16:04:36.398][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-07-26 16:04:36.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.403][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-07-26 16:04:36.404][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-07-26 16:04:36.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.408][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-07-26 16:04:36.410][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-07-26 16:04:36.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.414][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-07-26 16:04:36.415][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-07-26 16:04:36.418][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-07-26 16:04:36.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.423][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-07-26 16:04:36.424][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-07-26 16:04:36.425][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-07-26 16:04:36.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.430][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-07-26 16:04:36.432][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:36.433][self$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[2025-07-26 16:04:36.434][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.435][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:36.436][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.438][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.439][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:36.440][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.441][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-07-26 16:04:36.442][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:36.444][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.445][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-07-26 16:04:36.446][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:36.447][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.448][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.450][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:04:36.450][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-26 16:04:36.450][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-26 16:04:36.450][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-07-26 16:04:36.450][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-07-26 16:04:36.451][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:04:36.452][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:36.453][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:36.454][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:36.455][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:36.456][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:36.458][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.459][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.460][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:36.461][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:36.462][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:36.463][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.465][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-07-26 16:04:36.467][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:36.468][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-07-26 16:04:36.469][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.470][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:36.472][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.473][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.474][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:36.475][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.476][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-07-26 16:04:36.478][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:36.479][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.480][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-07-26 16:04:36.481][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:36.482][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.484][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.485][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:04:36.485][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-26 16:04:36.485][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-26 16:04:36.485][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-07-26 16:04:36.485][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-07-26 16:04:36.486][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:04:36.487][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:36.488][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:36.489][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:36.490][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:36.492][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:36.493][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.494][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.495][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:36.496][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:36.497][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:36.498][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.500][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-07-26 16:04:36.502][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.503][self$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[2025-07-26 16:04:36.504][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.505][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:36.507][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.508][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.509][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:36.510][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.511][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-07-26 16:04:36.512][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:36.514][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:36.515][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-07-26 16:04:36.516][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:36.517][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.518][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.520][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.521][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:04:36.522][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:36.523][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:36.524][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:36.526][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:36.527][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:36.528][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.529][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.530][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:36.531][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:36.532][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:36.534][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.535][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-07-26 16:04:36.537][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.538][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-07-26 16:04:36.539][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.541][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:36.542][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.543][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.544][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:36.545][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.546][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-07-26 16:04:36.548][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:36.549][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:36.550][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-07-26 16:04:36.551][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:36.553][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.554][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.555][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.556][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-26 16:04:36.557][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:36.558][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:36.560][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:36.561][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:36.562][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:36.563][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.564][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.565][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:36.566][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:36.568][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:36.569][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.570][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-26 16:04:36.571][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.572][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[2025-07-26 16:04:36.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.637][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[2025-07-26 16:04:36.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.666][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-07-26 16:04:36.667][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-07-26 16:04:36.669][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-07-26 16:04:36.671][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-07-26 16:04:36.672][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-07-26 16:04:36.674][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-07-26 16:04:36.675][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-07-26 16:04:36.677][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-07-26 16:04:36.678][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-07-26 16:04:36.680][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-07-26 16:04:36.681][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-07-26 16:04:36.683][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-07-26 16:04:36.684][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-07-26 16:04:36.686][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-07-26 16:04:36.688][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-07-26 16:04:36.689][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-07-26 16:04:36.691][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-07-26 16:04:36.692][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-07-26 16:04:36.694][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-07-26 16:04:36.695][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-07-26 16:04:36.697][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-07-26 16:04:36.698][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-07-26 16:04:36.700][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-07-26 16:04:36.702][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-07-26 16:04:36.703][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-07-26 16:04:36.705][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-07-26 16:04:36.706][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-07-26 16:04:36.708][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-07-26 16:04:36.709][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-07-26 16:04:36.711][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-07-26 16:04:36.712][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-07-26 16:04:36.714][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-07-26 16:04:36.716][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-07-26 16:04:36.717][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-07-26 16:04:36.719][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-07-26 16:04:36.720][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-07-26 16:04:36.722][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-07-26 16:04:36.723][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-07-26 16:04:36.725][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-07-26 16:04:36.726][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-07-26 16:04:36.728][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-07-26 16:04:36.730][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-07-26 16:04:36.732][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-07-26 16:04:36.734][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-07-26 16:04:36.737][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-07-26 16:04:36.738][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-07-26 16:04:36.740][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-07-26 16:04:36.742][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-07-26 16:04:36.743][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-07-26 16:04:36.745][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-07-26 16:04:36.746][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-07-26 16:04:36.748][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-07-26 16:04:36.749][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-07-26 16:04:36.751][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-07-26 16:04:36.753][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-07-26 16:04:36.754][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-07-26 16:04:36.756][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-07-26 16:04:36.763][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-07-26 16:04:36.765][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-07-26 16:04:36.767][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-07-26 16:04:36.768][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-07-26 16:04:36.770][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-07-26 16:04:36.771][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-07-26 16:04:36.773][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-07-26 16:04:36.774][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-07-26 16:04:36.776][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-07-26 16:04:36.777][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-07-26 16:04:36.779][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-07-26 16:04:36.780][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-07-26 16:04:36.782][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-07-26 16:04:36.784][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-07-26 16:04:36.785][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-07-26 16:04:36.787][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-07-26 16:04:36.788][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-07-26 16:04:36.790][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-07-26 16:04:36.791][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-07-26 16:04:36.793][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-07-26 16:04:36.794][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-07-26 16:04:36.796][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-07-26 16:04:36.797][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-07-26 16:04:36.799][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-07-26 16:04:36.800][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-07-26 16:04:36.802][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-07-26 16:04:36.804][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-07-26 16:04:36.806][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-07-26 16:04:36.807][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-26 16:04:36.808][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.810][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.841][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[2025-07-26 16:04:36.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.849][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.DEBUG[2025-07-26 16:04:36.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.856][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[2025-07-26 16:04:36.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-26 16:04:36.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:36.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:36.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:36.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:36.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:36.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-26 16:04:36.941][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-07-26 16:04:36.943][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-07-26 16:04:36.945][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.946][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-07-26 16:04:36.947][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.949][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:36.950][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.951][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.952][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.953][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.954][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-07-26 16:04:36.956][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:36.957][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.958][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-07-26 16:04:36.959][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:36.960][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-07-26 16:04:36.960][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-07-26 16:04:36.962][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:36.963][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.964][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-07-26 16:04:36.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:36.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:36.967][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:36.969][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:36.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:36.971][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.972][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-07-26 16:04:36.972][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-07-26 16:04:36.973][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:36.974][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:36.975][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.977][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:36.978][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-07-26 16:04:36.980][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.981][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-07-26 16:04:36.982][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.983][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:36.985][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.986][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.987][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.988][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:36.989][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-07-26 16:04:36.990][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:36.992][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:36.993][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-07-26 16:04:36.994][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:36.995][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-07-26 16:04:36.995][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-07-26 16:04:36.995][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-07-26 16:04:36.995][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-07-26 16:04:36.995][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-07-26 16:04:36.995][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-07-26 16:04:36.996][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:36.998][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:04:36.999][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-07-26 16:04:37.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:37.001][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:37.002][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:37.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:37.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:37.005][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:37.007][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-07-26 16:04:37.007][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-07-26 16:04:37.008][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:37.009][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:37.010][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:37.011][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:37.013][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-07-26 16:04:37.015][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:37.016][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-07-26 16:04:37.017][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:37.018][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:37.019][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:37.021][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:37.022][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:37.023][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:37.024][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-07-26 16:04:37.025][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:37.026][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:37.028][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-07-26 16:04:37.029][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:37.030][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-07-26 16:04:37.030][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:37.030][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:37.030][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:37.030][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:37.030][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:37.030][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:37.030][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:37.030][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:37.030][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:37.030][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-07-26 16:04:37.030][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:37.030][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:37.030][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-07-26 16:04:37.031][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:37.033][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-26 16:04:37.033][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-26 16:04:37.033][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-26 16:04:37.034][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-07-26 16:04:37.035][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:37.036][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:37.037][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:37.038][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:37.039][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:37.041][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:37.042][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-07-26 16:04:37.042][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-07-26 16:04:37.042][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-07-26 16:04:37.043][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:37.044][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:37.045][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:37.046][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-07-26 16:04:37.048][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-07-26 16:04:37.050][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:37.051][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-07-26 16:04:37.052][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:37.053][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-26 16:04:37.055][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:37.056][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-26 16:04:37.057][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:37.058][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-26 16:04:37.059][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-07-26 16:04:37.060][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-26 16:04:37.062][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:37.063][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-07-26 16:04:37.064][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-26 16:04:37.065][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-07-26 16:04:37.065][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-07-26 16:04:37.066][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-26 16:04:37.067][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-07-26 16:04:37.069][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-07-26 16:04:37.070][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:37.071][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:37.072][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-26 16:04:37.073][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-26 16:04:37.074][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-26 16:04:37.075][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-26 16:04:37.076][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-07-26 16:04:37.076][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-07-26 16:04:37.076][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-07-26 16:04:37.078][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-26 16:04:37.079][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-26 16:04:37.080][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-26 16:04:37.081][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-07-26 16:04:37.083][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-07-26 16:04:37.084][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-07-26 16:04:37.086][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-07-26 16:04:37.088][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-07-26 16:04:37.089][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-07-26 16:04:37.091][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-07-26 16:04:37.096][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2025-07-26 16:04:37.097][super$initialize] Register connector ncbi.pubchem.subst with the request scheduler
biodb.DEBUG[2025-07-26 16:04:37.099][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.pubchem.subst.
biodb.DEBUG[2025-07-26 16:04:37.101][private$addConnectorRules] Create new rule for URL "pubchem.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.subst".
biodb.DEBUG[2025-07-26 16:04:37.102][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-07-26 16:04:37.103][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-07-26 16:04:37.105][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.subst".
biodb.DEBUG[2025-07-26 16:04:37.106][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-07-26 16:04:37.107][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-07-26 16:04:37.109][rule$addConnector] Connector "ncbi.pubchem.subst" is already listed in rule "pubchem.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-07-26 16:04:37.114][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2025-07-26 16:04:37.119][biodb::testThat]
biodb.INFO [2025-07-26 16:04:37.121][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-07-26 16:04:37.122][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:37.123][biodb::testThat]
biodb.TRACE[2025-07-26 16:04:37.127][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2025-07-26 16:04:37.129][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:04:37.132][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-07-26 16:04:37.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:37.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:37.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:37.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:37.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:37.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:37.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-26 16:04:37.149][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.150][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.153][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.159][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.161][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.163][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.164][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.169][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.174][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.184][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:37.224][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2025-07-26 16:04:37.227][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:37.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:37.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.232][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:37.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:37.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.236][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:37.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:37.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.241][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:37.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:37.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.246][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:37.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:37.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.251][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:37.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:37.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.255][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:37.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:37.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.271][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.311][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.316][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.321][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.348][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.349][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.351][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.366][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.371][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.376][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.381][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.382][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.384][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.385][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.400][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.401][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.403][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.410][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.411][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.413][ef$get] fields variable is a list.
biodb.INFO [2025-07-26 16:04:37.425][biodb::testThat]
biodb.INFO [2025-07-26 16:04:37.426][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-07-26 16:04:37.427][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:37.428][biodb::testThat]
biodb.DEBUG[2025-07-26 16:04:37.431][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-07-26 16:04:37.433][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
biodb.TRACE[2025-07-26 16:04:37.436][cch$loadFileContent] Trying to load 1 files from cache: [1]: "3".
biodb.TRACE[2025-07-26 16:04:37.439][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-07-26 16:04:37.455][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75/3.xml".
biodb.DEBUG[2025-07-26 16:04:37.456][conn$getEntryContent] 1 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-07-26 16:04:37.458][self$createEntryFromContent] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-07-26 16:04:37.460][self$createEntryFromContent] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-07-26 16:04:37.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-26 16:04:37.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:37.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:37.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:37.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:37.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:37.474][FUN] Functions in observer BiodbConfig: [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[2025-07-26 16:04:37.476][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.478][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.480][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.486][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.487][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.490][ef$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.491][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-07-26 16:04:37.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.496][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.501][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.510][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-07-26 16:04:37.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-26 16:04:37.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-26 16:04:37.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-26 16:04:37.545][self$createEntryFromContent] Accession numbers: 3.
biodb.TRACE[2025-07-26 16:04:37.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-07-26 16:04:37.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-07-26 16:04:37.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-07-26 16:04:37.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-07-26 16:04:37.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-07-26 16:04:37.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-07-26 16:04:37.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-07-26 16:04:37.571][biodb::testThat]
biodb.INFO [2025-07-26 16:04:37.573][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-07-26 16:04:37.574][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:37.575][biodb::testThat]
biodb.INFO [2025-07-26 16:04:37.584][biodb::testThat]
biodb.INFO [2025-07-26 16:04:37.585][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-07-26 16:04:37.586][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:37.587][biodb::testThat]
biodb.WARN [2025-07-26 16:04:37.602][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-07-26 16:04:37.606][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-07-26 16:04:37.618][biodb::testThat]
biodb.INFO [2025-07-26 16:04:37.619][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-07-26 16:04:37.620][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:37.621][biodb::testThat]
biodb.TRACE[2025-07-26 16:04:37.642][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:37.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:37.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.647][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:37.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:37.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.658][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:37.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:37.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.663][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:37.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:37.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.668][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:37.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:37.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.672][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:37.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:37.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.677][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:37.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:37.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.690][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:37.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:37.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.695][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-07-26 16:04:37.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-07-26 16:04:37.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.700][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:37.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-07-26 16:04:37.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.705][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:37.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:37.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.709][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-26 16:04:37.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-26 16:04:37.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.714][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:37.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-26 16:04:37.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-26 16:04:37.719][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:37.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-26 16:04:37.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-26 16:04:37.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-07-26 16:04:37.731][biodb::testThat]
biodb.INFO [2025-07-26 16:04:37.733][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-07-26 16:04:37.734][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:37.736][biodb::testThat]
biodb.INFO [2025-07-26 16:04:37.746][biodb::testThat]
biodb.INFO [2025-07-26 16:04:37.748][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-07-26 16:04:37.749][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:37.750][biodb::testThat]
biodb.INFO [2025-07-26 16:04:37.761][biodb::testThat]
biodb.INFO [2025-07-26 16:04:37.762][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-07-26 16:04:37.763][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:37.764][biodb::testThat]
biodb.DEBUG[2025-07-26 16:04:37.769][function(conn, opt)] Trying to download "https://pubchem.ncbi.nlm.nih.gov/substance/3".
biodb.DEBUG[2025-07-26 16:04:37.890][getUrlContent] Use RCurl for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/substance/3.
biodb.INFO [2025-07-26 16:04:37.969][biodb::testThat]
biodb.INFO [2025-07-26 16:04:37.971][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-07-26 16:04:37.972][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-26 16:04:37.973][biodb::testThat]
biodb.DEBUG[2025-07-26 16:04:38.100][getUrlContent] Use RCurl for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?sid=3&t=l.
biodb.INFO [2025-07-26 16:04:38.174][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-07-26 16:04:38.176][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.pubchem.subst from the request scheduler
biodb.INFO [2025-07-26 16:04:38.177][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2025-07-26 16:04:38.178][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-07-26 16:04:38.180][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-26 16:04:38.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-26 16:04:38.182][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-26 16:04:38.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-26 16:04:38.184][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-07-26 16:04:38.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 29 | WARN 1 | SKIP 0 | PASS 714 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_ccds.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 = `<NcbCcdsC>`, 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_100_ccds.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 = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure ('test_long_100_ccds.R:37:1'): We can load an entry from the database. ──
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")
── Failure ('test_long_200_gene.R:37:1'): Entry fields have a correct value ────
ef$get(f)$isVirtual() || e$hasField(f) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Field "sequence" cannot be found inside ncbi.gene entry 2833.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─biodb:::checkEntryFields(...)
 4.     └─testthat::expect_true(...)
── Failure ('test_long_200_gene.R:37:1'): Entry fields have a correct value ────
`w` not identical to `v`.
1/1 mismatches
x[1]: NA
y[1]: "ATGGTCCTTGAGGTGAGTGACCACCAAGTGCTAAATGACGCCGAGGTTGCCGCCCTCCTGGAGAACTTCAGCT
y[1]: CTTCCTATGACTATGGAGAAAACGAGAGTGACTCGTGCTGTACCTCCCCGCCCTGCCCACAGGACTTCAGCCTG
y[1]: AACTTCGACCGGGCCTTCCTGCCAGCCCTCTACAGCCTCCTCTTTCTGCTGGGGCTGCTGGGCAACGGCGCGGT
y[1]: GGCAGCCGTGCTGCTGAGCCGGCGGACAGCCCTGAGCAGCACCGACACCTTCCTGCTCCACCTAGCTGTAGCAG
y[1]: ACACGCTGCTGGTGCTGACACTGCCGCTCTGGGCAGTGGACGCTGCCGTCCAGTGGGTCTTTGGCTCTGGC...
Value of field "sequence" for database ncbi.gene entry 2833 ([1]: "NA") is different in reference entry ([1]: "ATGGTCCTTGAGGTGAGTGACCACCAAGTGCTAAATGACGCCGAGGTTGCCGCCCTCCTGGAGAACTTCAGCTCTTCCTATGACTATGGAGAAAACGAGAGTGACTCGTGCTGTACCTCCCCGCCCTGCCCACAGGACTTCAGCCTGAACTTCGACCGGGCCTTCCTGCCAGCCCTCTACAGCCTCCTCTTTCTGCTGGGGCTGCTGGGCAACGGCGCGGTGGCAGCCGTGCTGCTGAGCCGGCGGACAGCCCTGAGCAGCACCGACACCTTCCTGCTCCACCTAGCTGTAGCAGACACGCTGCTGGTGCTGACACTGCCGCTCTGGGCAGTGGACGCTGCCGTCCAGTGGGTCTTTGGCTCTGGCCTCTGCAAAGTGGCAGGTGCCCTCTTCAACATCAACTTCTACGCAGGAGCCCTCCTGCTGGCCTGCATCAGCTTTGACCGCTACCTGAACATAGTTCATGCCACCCAGCTCTACCGCCGGGGGCCCCCGGCCCGCGTGACCCTCACCTGCCTGGCTGTCTGGGGGCTCTGCCTGCTTTTCGCCCTCCCAGACTTCATCTTCCTGTCGGCCCACCACGACGAGCGCCTCAACGCCACCCACTGCCAATACAACTTCCCACAGGTGGGCCGCACGGCTCTGCGGGTGCTGCAGCTGGTGGCTGGCTTTCTGCTGCCCCTGCTGGTCATGGCCTACTGCTATGCCCACATCCTGGCCGTGCTGCTGGTTTCCAGGGGCCAGCGGCGCCTGCGGGCCATGCGGCTGGTGGTGGTGGTCGTGGTGGCCTTTGCCCTCTGCTGGACCCCCTATCACCTGGTGGTGCTGGTGGACATCCTCATGGACCTGGGCGCTTTGGCCCGCAACTGTGGCCGAGAAAGCAGGGTAGACGTGGCCAAGTCGGTCACCTCAGGCCTGGGCTACATGCACTGCTGCCTCAACCCGCTGCTCTATGCCTTTGTAGGGGTCAAGTTCCGGGAGCGGATGTGGATGCTGCTCTTGCGCCTGGGCTGCCCCAACCAGAGAGGGCTCCAGAGGCAGCCATCGTCTTCCCGCCGGGATTCATCCTGGTCTGAGACCTCAGAGGCCTCCTACTCGGGCTTGTGA").
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─biodb:::checkEntryFields(...)
 4.     └─testthat::expect_identical(...)
── Failure ('test_long_200_gene.R:37:1'): Entry fields have a correct value ────
ef$get(f)$isVirtual() || e$hasField(f) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Field "sequence" cannot be found inside ncbi.gene entry 3002.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─biodb:::checkEntryFields(...)
 4.     └─testthat::expect_true(...)
── Failure ('test_long_200_gene.R:37:1'): Entry fields have a correct value ────
`w` not identical to `v`.
1/1 mismatches
x[1]: NA
y[1]: "ATGCAACCAATCCTGCTTCTGCTGGCCTTCCTCCTGCTGCCCAGGGCAGATGCAGGGGAGATCATCGGGGGAC
y[1]: ATGAGGCCAAGCCCCACTCCCGCCCCTACATGGCTTATCTTATGATCTGGGATCAGAAGTCTCTGAAGAGGTGC
y[1]: GGTGGCTTCCTGATACGAGACGACTTCGTGCTGACAGCTGCTCACTGTTGGGGAAGCTCCATAAATGTCACCTT
y[1]: GGGGGCCCACAATATCAAAGAACAGGAGCCGACCCAGCAGTTTATCCCTGTGAAAAGACCCATCCCCCATCCAG
y[1]: CCTATAATCCTAAGAACTTCTCCAACGACATCATGCTACTGCAGCTGGAGAGAAAGGCCAAGCGGACCAGA...
Value of field "sequence" for database ncbi.gene entry 3002 ([1]: "NA") is different in reference entry ([1]: "ATGCAACCAATCCTGCTTCTGCTGGCCTTCCTCCTGCTGCCCAGGGCAGATGCAGGGGAGATCATCGGGGGACATGAGGCCAAGCCCCACTCCCGCCCCTACATGGCTTATCTTATGATCTGGGATCAGAAGTCTCTGAAGAGGTGCGGTGGCTTCCTGATACGAGACGACTTCGTGCTGACAGCTGCTCACTGTTGGGGAAGCTCCATAAATGTCACCTTGGGGGCCCACAATATCAAAGAACAGGAGCCGACCCAGCAGTTTATCCCTGTGAAAAGACCCATCCCCCATCCAGCCTATAATCCTAAGAACTTCTCCAACGACATCATGCTACTGCAGCTGGAGAGAAAGGCCAAGCGGACCAGAGCTGTGCAGCCCCTCAGGCTACCTAGCAACAAGGCCCAGGTGAAGCCAGGGCAGACATGCAGTGTGGCCGGCTGGGGGCAGACGGCCCCCCTGGGAAAACACTCACACACACTACAAGAGGTGAAGATGACAGTGCAGGAAGATCGAAAGTGCGAATCTGACTTACGCCATTATTACGACAGTACCATTGAGTTGTGCGTGGGGGACCCAGAGATTAAAAAGACTTCCTTTAAGGGGGACTCTGGAGGCCCTCTTGTGTGTAACAAGGTGGCCCAGGGCATTGTCTCCTATGGACGAAACAATGGCATGCCTCCACGAGCCTGCACCAAAGTCTCAAGCTTTGTACACTGGATAAAGAAAACCATGAAACGCTACTAA").
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─biodb:::checkEntryFields(...)
 4.     └─testthat::expect_identical(...)
── Failure ('test_long_200_gene.R:37:1'): Entry fields have a correct value ────
ef$get(f)$isVirtual() || e$hasField(f) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Field "sequence" cannot be found inside ncbi.gene entry 3627.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─biodb:::checkEntryFields(...)
 4.     └─testthat::expect_true(...)
── Failure ('test_long_200_gene.R:37:1'): Entry fields have a correct value ────
`w` not identical to `v`.
1/1 mismatches
x[1]: NA
y[1]: "ATGAATCAAACTGCCATTCTGATTTGCTGCCTTATCTTTCTGACTCTAAGTGGCATTCAAGGAGTACCTCTCT
y[1]: CTAGAACTGTACGCTGTACCTGCATCAGCATTAGTAATCAACCTGTTAATCCAAGGTCTTTAGAAAAACTTGAA
y[1]: ATTATTCCTGCAAGCCAATTTTGTCCACGTGTTGAGATCATTGCTACAATGAAAAAGAAGGGTGAGAAGAGATG
y[1]: TCTGAATCCAGAATCGAAGGCCATCAAGAATTTACTGAAAGCAGTTAGCAAGGAAAGGTCTAAAAGATCTCCTT
y[1]: AA"
Value of field "sequence" for database ncbi.gene entry 3627 ([1]: "NA") is different in reference entry ([1]: "ATGAATCAAACTGCCATTCTGATTTGCTGCCTTATCTTTCTGACTCTAAGTGGCATTCAAGGAGTACCTCTCTCTAGAACTGTACGCTGTACCTGCATCAGCATTAGTAATCAACCTGTTAATCCAAGGTCTTTAGAAAAACTTGAAATTATTCCTGCAAGCCAATTTTGTCCACGTGTTGAGATCATTGCTACAATGAAAAAGAAGGGTGAGAAGAGATGTCTGAATCCAGAATCGAAGGCCATCAAGAATTTACTGAAAGCAGTTAGCAAGGAAAGGTCTAAAAGATCTCCTTAA").
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─biodb:::checkEntryFields(...)
 4.     └─testthat::expect_identical(...)
── Failure ('test_long_200_gene.R:37:1'): Entry fields have a correct value ────
ef$get(f)$isVirtual() || e$hasField(f) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Field "sequence" cannot be found inside ncbi.gene entry 4316.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─biodb:::checkEntryFields(...)
 4.     └─testthat::expect_true(...)
── Failure ('test_long_200_gene.R:37:1'): Entry fields have a correct value ────
`w` not identical to `v`.
1/1 mismatches
x[1]: NA
y[1]: "ATGCGACTCACCGTGCTGTGTGCTGTGTGCCTGCTGCCTGGCAGCCTGGCCCTGCCGCTGCCTCAGGAGGCGG
y[1]: GAGGCATGAGTGAGCTACAGTGGGAACAGGCTCAGGACTATCTCAAGAGATTTTATCTCTATGACTCAGAAACA
y[1]: AAAAATGCCAACAGTTTAGAAGCCAAACTCAAGGAGATGCAAAAATTCTTTGGCCTACCTATAACTGGAATGTT
y[1]: AAACTCCCGCGTCATAGAAATAATGCAGAAGCCCAGATGTGGAGTGCCAGATGTTGCAGAATACTCACTATTTC
y[1]: CAAATAGCCCAAAATGGACTTCCAAAGTGGTCACCTACAGGATCGTATCATATACTCGAGACTTACCGCAT...
Value of field "sequence" for database ncbi.gene entry 4316 ([1]: "NA") is different in reference entry ([1]: "ATGCGACTCACCGTGCTGTGTGCTGTGTGCCTGCTGCCTGGCAGCCTGGCCCTGCCGCTGCCTCAGGAGGCGGGAGGCATGAGTGAGCTACAGTGGGAACAGGCTCAGGACTATCTCAAGAGATTTTATCTCTATGACTCAGAAACAAAAAATGCCAACAGTTTAGAAGCCAAACTCAAGGAGATGCAAAAATTCTTTGGCCTACCTATAACTGGAATGTTAAACTCCCGCGTCATAGAAATAATGCAGAAGCCCAGATGTGGAGTGCCAGATGTTGCAGAATACTCACTATTTCCAAATAGCCCAAAATGGACTTCCAAAGTGGTCACCTACAGGATCGTATCATATACTCGAGACTTACCGCATATTACAGTGGATCGATTAGTGTCAAAGGCTTTAAACATGTGGGGCAAAGAGATCCCCCTGCATTTCAGGAAAGTTGTATGGGGAACTGCTGACATCATGATTGGCTTTGCGCGAGGAGCTCATGGGGACTCCTACCCATTTGATGGGCCAGGAAACACGCTGGCTCATGCCTTTGCGCCTGGGACAGGTCTCGGAGGAGATGCTCACTTCGATGAGGATGAACGCTGGACGGATGGTAGCAGTCTAGGGATTAACTTCCTGTATGCTGCAACTCATGAACTTGGCCATTCTTTGGGTATGGGACATTCCTCTGATCCTAATGCAGTGATGTATCCAACCTATGGAAATGGAGATCCCCAAAATTTTAAACTTTCCCAGGATGATATTAAAGGCATTCAGAAACTATATGGAAAGAGAAGTAATTCAAGAAAGAAATAG").
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─biodb:::checkEntryFields(...)
 4.     └─testthat::expect_identical(...)
── Failure ('test_long_200_gene.R:37:1'): Entry fields have a correct value ────
ef$get(f)$isVirtual() || e$hasField(f) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Field "sequence" cannot be found inside ncbi.gene entry 50943.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─biodb:::checkEntryFields(...)
 4.     └─testthat::expect_true(...)
── Failure ('test_long_200_gene.R:37:1'): Entry fields have a correct value ────
`w` not identical to `v`.
1/1 mismatches
x[1]: NA
y[1]: "ATGCCCAACCCCAGGCCTGGCAAGCCCTCGGCCCCTTCCTTGGCCCTTGGCCCATCCCCAGGAGCCTCGCCCA
y[1]: GCTGGAGGGCTGCACCCAAAGCCTCAGACCTGCTGGGGGCCCGGGGCCCAGGGGGAACCTTCCAGGGCCGAGAT
y[1]: CTTCGAGGCGGGGCCCATGCCTCCTCTTCTTCCTTGAACCCCATGCCACCATCGCAGCTGCAGCTGCCCACACT
y[1]: GCCCCTAGTCATGGTGGCACCCTCCGGGGCACGGCTGGGCCCCTTGCCCCACTTACAGGCACTCCTCCAGGACA
y[1]: GGCCACATTTCATGCACCAGCTCTCAACGGTGGATGCCCACGCCCGGACCCCTGTGCTGCAGGTGCACCCC...
Value of field "sequence" for database ncbi.gene entry 50943 ([1]: "NA") is different in reference entry ([1]: "ATGCCCAACCCCAGGCCTGGCAAGCCCTCGGCCCCTTCCTTGGCCCTTGGCCCATCCCCAGGAGCCTCGCCCAGCTGGAGGGCTGCACCCAAAGCCTCAGACCTGCTGGGGGCCCGGGGCCCAGGGGGAACCTTCCAGGGCCGAGATCTTCGAGGCGGGGCCCATGCCTCCTCTTCTTCCTTGAACCCCATGCCACCATCGCAGCTGCAGCTGCCCACACTGCCCCTAGTCATGGTGGCACCCTCCGGGGCACGGCTGGGCCCCTTGCCCCACTTACAGGCACTCCTCCAGGACAGGCCACATTTCATGCACCAGCTCTCAACGGTGGATGCCCACGCCCGGACCCCTGTGCTGCAGGTGCACCCCCTGGAGAGCCCAGCCATGATCAGCCTCACACCACCCACCACCGCCACTGGGGTCTTCTCCCTCAAGGCCCGGCCTGGCCTCCCACCTGGGATCAACGTGGCCAGCCTGGAATGGGTGTCCAGGGAGCCGGCACTGCTCTGCACCTTCCCAAATCCCAGTGCACCCAGGAAGGACAGCACCCTTTCGGCTGTGCCCCAGAGCTCCTACCCACTGCTGGCAAATGGTGTCTGCAAGTGGCCCGGATGTGAGAAGGTCTTCGAAGAGCCAGAGGACTTCCTCAAGCACTGCCAGGCGGACCATCTTCTGGATGAGAAGGGCAGGGCACAATGTCTCCTCCAGAGAGAGATGGTACAGTCTCTGGAGCAGCAGCTGGTGCTGGAGAAGGAGAAGCTGAGTGCCATGCAGGCCCACCTGGCTGGGAAAATGGCACTGACCAAGGCTTCATCTGTGGCATCATCCGACAAGGGCTCCTGCTGCATCGTAGCTGCTGGCAGCCAAGGCCCTGTCGTCCCAGCCTGGTCTGGCCCCCGGGAGGCCCCTGACAGCCTGTTTGCTGTCCGGAGGCACCTGTGGGGTAGCCATGGAAACAGCACATTCCCAGAGTTCCTCCACAACATGGACTACTTCAAGTTCCACAACATGCGACCCCCTTTCACCTACGCCACGCTCATCCGCTGGGCCATCCTGGAGGCTCCAGAGAAGCAGCGGACACTCAATGAGATCTACCACTGGTTCACACGCATGTTTGCCTTCTTCAGAAACCATCCTGCCACCTGGAAGAACGCCATCCGCCACAACCTGAGTCTGCACAAGTGCTTTGTGCGGGTGGAGAGCGAGAAGGGGGCTGTGTGGACCGTGGATGAGCTGGAGTTCCGCAAGAAACGGAGCCAGAGGCCCAGCAGGTGTTCCAACCCTACACCTGGCCCCTGA").
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─biodb:::checkEntryFields(...)
 4.     └─testthat::expect_identical(...)
── Failure ('test_long_200_gene.R:37:1'): Entry fields have a correct value ────
ef$get(f)$isVirtual() || e$hasField(f) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Field "sequence" cannot be found inside ncbi.gene entry 5551.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─biodb:::checkEntryFields(...)
 4.     └─testthat::expect_true(...)
── Failure ('test_long_200_gene.R:37:1'): Entry fields have a correct value ────
`w` not identical to `v`.
1/1 mismatches
x[1]: NA
y[1]: "ATGGCAGCCCGTCTGCTCCTCCTGGGCATCCTTCTCCTGCTGCTGCCCCTGCCCGTCCCTGCCCCGTGCCACA
y[1]: CAGCCGCACGCTCAGAGTGCAAGCGCAGCCACAAGTTCGTGCCTGGTGCATGGCTGGCCGGGGAGGGTGTGGAC
y[1]: GTGACCAGCCTCCGCCGCTCGGGCTCCTTCCCAGTGGACACACAAAGGTTCCTGCGGCCCGACGGCACCTGCAC
y[1]: CCTCTGTGAAAATGCCCTACAGGAGGGCACCCTCCAGCGCCTGCCTCTGGCGCTCACCAACTGGCGGGCCCAGG
y[1]: GCTCTGGCTGCCAGCGCCATGTAACCAGGGCCAAAGTCAGCTCCACTGAAGCTGTGGCCCGGGATGCGGCT...
Value of field "sequence" for database ncbi.gene entry 5551 ([1]: "NA") is different in reference entry ([1]: "ATGGCAGCCCGTCTGCTCCTCCTGGGCATCCTTCTCCTGCTGCTGCCCCTGCCCGTCCCTGCCCCGTGCCACACAGCCGCACGCTCAGAGTGCAAGCGCAGCCACAAGTTCGTGCCTGGTGCATGGCTGGCCGGGGAGGGTGTGGACGTGACCAGCCTCCGCCGCTCGGGCTCCTTCCCAGTGGACACACAAAGGTTCCTGCGGCCCGACGGCACCTGCACCCTCTGTGAAAATGCCCTACAGGAGGGCACCCTCCAGCGCCTGCCTCTGGCGCTCACCAACTGGCGGGCCCAGGGCTCTGGCTGCCAGCGCCATGTAACCAGGGCCAAAGTCAGCTCCACTGAAGCTGTGGCCCGGGATGCGGCTCGTAGCATCCGCAACGACTGGAAGGTCGGGCTGGACGTGACTCCTAAGCCCACCAGCAATGTGCATGTGTCTGTGGCCGGCTCACACTCACAGGCAGCCAACTTTGCAGCCCAGAAGACCCACCAGGACCAGTACAGCTTCAGCACTGACACGGTGGAGTGCCGCTTCTACAGTTTCCATGTGGTACACACTCCCCCGCTGCACCCTGACTTCAAGAGGGCCCTCGGGGACCTGCCCCACCACTTCAACGCCTCCACCCAGCCCGCCTACCTCAGGCTTATCTCCAACTACGGCACCCACTTCATCCGGGCTGTGGAGCTGGGTGGCCGCATATCGGCCCTCACTGCCCTGCGCACCTGCGAGCTGGCCCTGGAAGGGCTCACGGACAACGAGGTGGAGGACTGCCTGACTGTCGAGGCCCAGGTCAACATAGGCATCCACGGCAGCATCTCTGCCGAAGCCAAGGCCTGTGAGGAGAAGAAGAAGAAGCACAAGATGACGGCCTCCTTCCACCAAACCTACCGGGAGCGCCACTCGGAAGTGGTTGGCGGCCATCACACCTCCATTAACGACCTGCTGTTCGGGATCCAGGCCGGGCCCGAGCAGTACTCAGCCTGGGTAAACTCGCTGCCCGGCAGCCCTGGCCTGGTGGACTACACCCTGGAACCCCTGCACGTGCTGCTGGACAGCCAGGACCCGCGGCGGGAGGCACTGAGGAGGGCCCTGAGTCAGTACCTGACGGACAGGGCTCGCTGGAGGGACTGCAGCCGGCCGTGCCCACCAGGGCGGCAGAAGAGCCCCCGAGACCCATGCCAGTGTGTGTGCCATGGCTCAGCGGTCACCACCCAGGACTGCTGCCCTCGGCAGAGGGGCCTGGCCCAGCTGGAGGTGACCTTCATCCAAGCATGGGGCCTGTGGGGGGACTGGTTCACTGCCACGGATGCCTATGTGAAGCTCTTCTTTGGTGGCCAGGAGCTGAGGACGAGCACCGTGTGGGACAATAACAACCCCATCTGGTCAGTGCGGCTGGATTTTGGGGATGTGCTCCTGGCCACAGGGGGGCCCCTGAGGTTGCAGGTCTGGGATCAGGACTCTGGCAGGGACGATGACCTCCTTGGCACCTGTGATCAGGCTCCCAAGTCTGGTTCCCATGAGGTGAGATGCAACCTGAATCATGGCCACCTAAAATTCCGCTATCATGCCAGGTGCTTGCCCCACCTGGGAGGAGGCACCTGCCTGGACTATGTCCCCCAAATGCTTCTGGGGGAGCCTCCAGGAAACCGGAGTGGGGCCGTGTGGTGA").
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─biodb:::checkEntryFields(...)
 4.     └─testthat::expect_identical(...)
── Failure ('test_long_200_gene.R:37:1'): Entry fields have a correct value ────
ef$get(f)$isVirtual() || e$hasField(f) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Field "sequence" cannot be found inside ncbi.gene entry 916.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─biodb:::checkEntryFields(...)
 4.     └─testthat::expect_true(...)
── Failure ('test_long_200_gene.R:37:1'): Entry fields have a correct value ────
`w` not identical to `v`.
1/1 mismatches
x[1]: NA
y[1]: "ATGCAGTCGGGCACTCACTGGAGAGTTCTGGGCCTCTGCCTCTTATCAGTTGGCGTTTGGGGGCAAGATGGTA
y[1]: ATGAAGAAATGGGTGGTATTACACAGACACCATATAAAGTCTCCATCTCTGGAACCACAGTAATATTGACATGC
y[1]: CCTCAGTATCCTGGATCTGAAATACTATGGCAACACAATGATAAAAACATAGGCGGTGATGAGGATGATAAAAA
y[1]: CATAGGCAGTGATGAGGATCACCTGTCACTGAAGGAATTTTCAGAATTGGAGCAAAGTGGTTATTATGTCTGCT
y[1]: ACCCCAGAGGAAGCAAACCAGAAGATGCGAACTTTTATCTCTACCTGAGGGCAAGAGTGTGTGAGAACTGC...
Value of field "sequence" for database ncbi.gene entry 916 ([1]: "NA") is different in reference entry ([1]: "ATGCAGTCGGGCACTCACTGGAGAGTTCTGGGCCTCTGCCTCTTATCAGTTGGCGTTTGGGGGCAAGATGGTAATGAAGAAATGGGTGGTATTACACAGACACCATATAAAGTCTCCATCTCTGGAACCACAGTAATATTGACATGCCCTCAGTATCCTGGATCTGAAATACTATGGCAACACAATGATAAAAACATAGGCGGTGATGAGGATGATAAAAACATAGGCAGTGATGAGGATCACCTGTCACTGAAGGAATTTTCAGAATTGGAGCAAAGTGGTTATTATGTCTGCTACCCCAGAGGAAGCAAACCAGAAGATGCGAACTTTTATCTCTACCTGAGGGCAAGAGTGTGTGAGAACTGCATGGAGATGGATGTGATGTCGGTGGCCACAATTGTCATAGTGGACATCTGCATCACTGGGGGCTTGCTGCTGCTGGTTTACTACTGGAGCAAGAATAGAAAGGCCAAGGCCAAGCCTGTGACACGAGGAGCGGGTGCTGGCGGCAGGCAAAGGGGACAAAACAAGGAGAGGCCACCACCTGTTCCCAACCCAGACTATGAGCCCATCCGGAAAGGCCAGCGGGACCTGTATTCTGGCCTGAATCAGAGACGCATCTGA").
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─biodb:::checkEntryFields(...)
 4.     └─testthat::expect_identical(...)
── Error ('test_long_200_gene.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 = `<NcbGnCnn>`, 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_200_gene.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 = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_200_gene.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 = `<NcbGnCnn>`, opt = `<named list>`)
── Failure ('test_long_200_gene.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 = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_200_gene.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 = `<NcbGnCnn>`, opt = `<named list>`)
── Failure ('test_long_200_gene.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 = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure ('test_long_200_gene.R:37:1'): We can load an entry from the database. ──
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() accepts a single vector. ──
Error in `if (file == "" || length(file) == 0) stop("empty or no content specified")`: missing value where TRUE/FALSE needed
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$annotateMzValues(...)
 4.     └─self$searchForEntries(fieldsFilter, max.results = max.results)
 5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
 6.         └─self$wsEsearch(term = term, retmax = retmax, retfmt = "ids")
 7.           └─XML::xmlInternalTreeParse(results, asText = TRUE)
── Error ('test_long_300_pubchem.comp.R:37:1'): ppm tolerance works in annotateMzValues() ──
Error in `if (file == "" || length(file) == 0) stop("empty or no content specified")`: missing value where TRUE/FALSE needed
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$annotateMzValues(...)
 4.     └─self$searchForEntries(fieldsFilter, max.results = max.results)
 5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
 6.         └─self$wsEsearch(term = term, retmax = retmax, retfmt = "ids")
 7.           └─XML::xmlInternalTreeParse(results, asText = TRUE)
── Error ('test_long_300_pubchem.comp.R:37:1'): Input data frame is not modified by annotateMzValues() ──
Error in `if (file == "" || length(file) == 0) stop("empty or no content specified")`: missing value where TRUE/FALSE needed
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$annotateMzValues(...)
 4.     └─self$searchForEntries(fieldsFilter, max.results = max.results)
 5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
 6.         └─self$wsEsearch(term = term, retmax = retmax, retfmt = "ids")
 7.           └─XML::xmlInternalTreeParse(results, asText = TRUE)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() works correctly with real values. ──
Error in `if (file == "" || length(file) == 0) stop("empty or no content specified")`: missing value where TRUE/FALSE needed
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$annotateMzValues(...)
 4.     └─self$searchForEntries(fieldsFilter, max.results = max.results)
 5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
 6.         └─self$wsEsearch(term = term, retmax = retmax, retfmt = "ids")
 7.           └─XML::xmlInternalTreeParse(results, asText = TRUE)
── Error ('test_long_300_pubchem.comp.R:37:1'): Additional fields are accepted in annotateMzValues() ──
Error in `if (file == "" || length(file) == 0) stop("empty or no content specified")`: missing value where TRUE/FALSE needed
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$annotateMzValues(...)
 4.     └─self$searchForEntries(fieldsFilter, max.results = max.results)
 5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
 6.         └─self$wsEsearch(term = term, retmax = retmax, retfmt = "ids")
 7.           └─XML::xmlInternalTreeParse(results, asText = TRUE)

[ FAIL 29 | WARN 1 | SKIP 0 | PASS 714 ]
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 4.5.1 (2025-06-13 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:
  ── Error ('test_long_300_pubchem.comp.R:37:1'): Additional fields are accepted in annotateMzValues() ──
  Error in `if (file == "" || length(file) == 0) stop("empty or no content specified")`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
   3.   └─conn$annotateMzValues(...)
   4.     └─self$searchForEntries(fieldsFilter, max.results = max.results)
   5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
   6.         └─self$wsEsearch(term = term, retmax = retmax, retfmt = "ids")
   7.           └─XML::xmlInternalTreeParse(results, asText = TRUE)
  
  [ FAIL 29 | WARN 1 | SKIP 0 | PASS 714 ]
  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)