Back to Long Tests report for BioC 3.20

This page was generated on 2025-03-01 23:55 -0500 (Sat, 01 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4768
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4503
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4526
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 10/32HostnameOS / ArchCHECK
biodbNcbi 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-03-01 09:55 -0500 (Sat, 01 Mar 2025)
git_url: https://git.bioconductor.org/packages/biodbNcbi
git_branch: RELEASE_3_20
git_last_commit: b6b4ed9
git_last_commit_date: 2024-10-29 11:09:30 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

CHECK results for biodbNcbi on palomino8

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: 1.10.0
Command: F:\biocbuild\bbs-3.20-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_1.10.0.tar.gz
StartedAt: 2025-03-01 16:04:58 -0500 (Sat, 01 Mar 2025)
EndedAt: 2025-03-01 16:27:34 -0500 (Sat, 01 Mar 2025)
EllapsedTime: 1355.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNcbi.Rcheck
Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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Type 'license()' or 'licence()' for distribution details.

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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 [2025-03-01 16:05:48.644][biodb::testContext]
biodb.INFO [2025-03-01 16:05:48.705][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:05:48.706][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2025-03-01 16:05:48.708][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:05:48.709][biodb::testContext]
biodb.INFO [2025-03-01 16:05:48.729][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:05:48.732][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-01 16:05:48.776][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:05:48.777][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-01 16:05:48.778][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-01 16:05:48.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:48.783][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-01 16:05:48.799][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-01 16:05:48.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:48.803][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-01 16:05:48.804][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-01 16:05:48.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:48.809][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-01 16:05:48.810][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-01 16:05:48.811][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-01 16:05:48.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.814][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[2025-03-01 16:05:48.815][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-01 16:05:48.817][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-01 16:05:48.818][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-01 16:05:48.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:48.822][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-01 16:05:48.823][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-01 16:05:48.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:48.828][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-01 16:05:48.829][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-01 16:05:48.830][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-01 16:05:48.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:48.834][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-01 16:05:48.836][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-01 16:05:48.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:48.840][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-01 16:05:48.841][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-01 16:05:48.842][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-01 16:05:48.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:48.847][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:05:48.848][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-01 16:05:48.849][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-01 16:05:48.850][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-01 16:05:48.851][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-01 16:05:48.852][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-01 16:05:48.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.856][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[2025-03-01 16:05:48.857][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-01 16:05:48.858][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-01 16:05:48.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:48.862][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-01 16:05:48.864][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-01 16:05:48.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:48.868][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-01 16:05:48.869][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-01 16:05:48.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:48.873][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-01 16:05:48.875][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-01 16:05:48.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.878][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[2025-03-01 16:05:48.879][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-01 16:05:48.880][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-01 16:05:48.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:48.884][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:05:48.886][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-01 16:05:48.889][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-01 16:05:48.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.892][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[2025-03-01 16:05:48.894][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-01 16:05:48.895][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-01 16:05:48.896][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-01 16:05:48.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:48.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:48.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:48.902][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-01 16:05:48.937][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:48.951][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-01 16:05:48.952][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:48.953][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:48.955][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:48.957][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:48.958][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:48.959][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:48.960][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:05:48.962][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:48.963][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:48.964][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-01 16:05:48.965][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:48.966][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:48.968][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:48.969][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:05:48.969][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:05:48.969][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:05:48.969][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:05:48.969][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:05:48.970][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:48.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:48.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:48.974][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:48.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:48.976][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:48.977][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:48.978][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:48.979][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:48.980][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:48.982][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:48.983][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:48.984][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-01 16:05:48.986][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:48.987][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:05:48.989][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:48.990][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:48.991][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:48.992][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:48.993][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:48.994][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:48.996][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:05:48.997][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:48.998][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:48.999][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-01 16:05:49.000][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:49.002][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:49.003][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.004][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:05:49.004][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:05:49.004][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:05:49.004][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:05:49.004][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:05:49.005][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:49.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:49.007][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:49.009][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:49.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:49.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:49.012][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.013][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:49.014][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:49.015][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:49.017][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:49.018][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:49.019][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-01 16:05:49.021][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.022][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-01 16:05:49.023][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.025][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:49.026][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.027][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.028][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:49.029][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.030][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:05:49.032][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:49.033][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:49.034][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-01 16:05:49.035][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:49.036][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:49.038][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.039][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:49.040][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:49.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:49.042][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:49.043][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:49.045][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:49.046][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:49.047][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.048][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:49.049][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:49.050][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:49.051][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:49.053][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:49.054][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-01 16:05:49.056][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.057][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:05:49.058][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.059][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:49.061][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.062][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.063][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:49.064][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.065][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:05:49.067][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:49.068][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:49.069][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-01 16:05:49.070][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:49.071][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:49.073][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.074][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:49.075][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:49.076][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:49.077][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:49.078][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:49.079][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:49.080][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:49.082][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.083][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:49.084][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:49.085][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:49.086][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:49.087][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:49.091][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:05:49.092][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.120][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[2025-03-01 16:05:49.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.135][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[2025-03-01 16:05:49.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.157][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[2025-03-01 16:05:49.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.173][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[2025-03-01 16:05:49.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.190][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-01 16:05:49.194][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-01 16:05:49.195][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-01 16:05:49.197][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-01 16:05:49.198][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-01 16:05:49.200][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-01 16:05:49.202][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-01 16:05:49.203][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-01 16:05:49.205][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-01 16:05:49.206][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-01 16:05:49.208][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-01 16:05:49.209][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-01 16:05:49.211][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-01 16:05:49.212][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-01 16:05:49.214][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:05:49.215][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:05:49.217][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-01 16:05:49.219][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-01 16:05:49.220][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-01 16:05:49.222][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-01 16:05:49.223][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-01 16:05:49.225][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-01 16:05:49.226][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-01 16:05:49.228][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-01 16:05:49.229][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-01 16:05:49.231][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-01 16:05:49.232][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-01 16:05:49.234][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-01 16:05:49.236][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-01 16:05:49.237][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-01 16:05:49.239][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-01 16:05:49.240][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-01 16:05:49.242][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-01 16:05:49.243][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-01 16:05:49.245][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-01 16:05:49.246][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-01 16:05:49.248][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-01 16:05:49.249][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-01 16:05:49.251][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-01 16:05:49.253][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-01 16:05:49.254][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-01 16:05:49.256][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-01 16:05:49.257][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-01 16:05:49.259][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-01 16:05:49.260][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-01 16:05:49.262][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:05:49.263][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-01 16:05:49.265][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-01 16:05:49.267][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-01 16:05:49.268][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-01 16:05:49.270][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-01 16:05:49.271][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-01 16:05:49.273][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-01 16:05:49.274][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-01 16:05:49.276][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-01 16:05:49.277][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-01 16:05:49.279][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-01 16:05:49.280][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-01 16:05:49.282][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-01 16:05:49.283][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-01 16:05:49.285][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-01 16:05:49.286][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-01 16:05:49.288][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-01 16:05:49.290][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-01 16:05:49.291][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-01 16:05:49.293][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-01 16:05:49.294][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-01 16:05:49.296][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-01 16:05:49.297][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-01 16:05:49.299][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-01 16:05:49.300][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-01 16:05:49.302][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-01 16:05:49.303][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-01 16:05:49.305][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-01 16:05:49.307][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-01 16:05:49.308][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-01 16:05:49.310][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-01 16:05:49.311][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-01 16:05:49.313][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-01 16:05:49.314][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-01 16:05:49.316][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-01 16:05:49.317][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-01 16:05:49.319][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-01 16:05:49.352][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-01 16:05:49.355][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:05:49.358][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:05:49.365][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.367][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.446][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[2025-03-01 16:05:49.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:49.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:49.501][bdb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-03-01 16:05:49.536][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-03-01 16:05:49.539][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.540][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-03-01 16:05:49.541][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.542][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:49.543][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.545][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.546][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.547][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.548][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-03-01 16:05:49.549][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:49.551][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.552][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-03-01 16:05:49.553][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:49.554][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-03-01 16:05:49.554][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-03-01 16:05:49.555][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:49.557][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:49.558][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:05:49.559][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:49.560][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:49.561][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:49.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:49.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:49.564][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.566][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-03-01 16:05:49.566][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-03-01 16:05:49.567][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:49.568][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:49.569][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.570][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:49.572][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-03-01 16:05:49.574][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.575][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-03-01 16:05:49.576][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.577][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:49.578][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.580][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.581][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.582][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.583][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-01 16:05:49.585][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:49.586][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.587][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-03-01 16:05:49.588][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:49.589][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-03-01 16:05:49.589][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-03-01 16:05:49.589][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-03-01 16:05:49.589][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-03-01 16:05:49.589][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-03-01 16:05:49.589][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-03-01 16:05:49.591][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:49.617][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:05:49.619][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:05:49.620][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:49.621][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:49.622][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:49.624][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:49.625][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:49.626][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.627][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-03-01 16:05:49.627][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-03-01 16:05:49.628][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:49.629][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:49.630][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.631][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:49.633][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-03-01 16:05:49.635][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:49.636][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-03-01 16:05:49.637][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.638][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:49.639][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.641][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.642][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.643][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.644][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-01 16:05:49.645][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:49.646][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.648][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-03-01 16:05:49.649][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:49.650][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-03-01 16:05:49.650][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:05:49.650][self$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[2025-03-01 16:05:49.650][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:05:49.650][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:05:49.650][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:05:49.650][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:05:49.650][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:05:49.650][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:05:49.650][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:05:49.650][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-03-01 16:05:49.650][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:05:49.650][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:05:49.650][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:05:49.651][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:49.653][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:05:49.653][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:05:49.653][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:05:49.654][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-03-01 16:05:49.655][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:49.656][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:49.657][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:49.658][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:49.659][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:49.661][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.662][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-03-01 16:05:49.662][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-03-01 16:05:49.662][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-03-01 16:05:49.663][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:49.664][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:49.665][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.666][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-03-01 16:05:49.668][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-03-01 16:05:49.670][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.671][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-03-01 16:05:49.672][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.673][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:49.675][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.679][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.681][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.682][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.683][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-01 16:05:49.684][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:49.685][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.687][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-03-01 16:05:49.688][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:49.689][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-03-01 16:05:49.689][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-03-01 16:05:49.690][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:49.691][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:49.693][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-03-01 16:05:49.694][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:49.695][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:49.696][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:49.697][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:49.698][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:49.699][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:49.700][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-03-01 16:05:49.700][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-03-01 16:05:49.700][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-03-01 16:05:49.702][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:49.703][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:49.704][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:49.705][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-03-01 16:05:49.710][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-03-01 16:05:49.712][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:05:49.714][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:05:49.715][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-03-01 16:05:49.717][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:05:49.719][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-03-01 16:05:49.753][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-03-01 16:05:49.755][initialize] Register connector ncbi.ccds with the request scheduler
biodb.DEBUG[2025-03-01 16:05:49.758][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.ccds.
biodb.DEBUG[2025-03-01 16:05:49.762][private$addConnectorRules] Create new rule for URL "www.ncbi.nlm.nih.gov" of connector "ncbi.ccds".
biodb.DEBUG[2025-03-01 16:05:49.766][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:05:49.767][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:05:49.769][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.ccds".
biodb.DEBUG[2025-03-01 16:05:49.770][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:05:49.772][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:05:49.773][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2025-03-01 16:05:49.783][biodb::testThat]
biodb.INFO [2025-03-01 16:05:49.784][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-01 16:05:49.785][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:49.786][biodb::testThat]
biodb.TRACE[2025-03-01 16:05:49.854][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2025-03-01 16:05:49.857][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:05:49.860][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-03-01 16:05:49.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:05:49.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:49.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:49.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:49.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:49.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:49.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:05:49.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:49.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:49.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:49.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:49.984][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:05:50.006][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.008][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.031][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:05:50.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.037][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.041][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.051][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:05:50.112][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2025-03-01 16:05:50.115][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.124][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.148][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:50.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:50.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.153][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:50.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:50.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.158][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:50.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:50.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.162][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:50.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:50.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.293][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.334][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.339][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.343][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.442][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.443][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.451][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.467][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:05:50.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.472][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.476][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.481][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:05:50.482][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.485][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.486][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:05:50.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.500][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.501][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.504][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.510][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.511][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.513][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.633][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2025-03-01 16:05:50.666][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:05:50.668][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-03-01 16:05:50.669][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:05:50.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:50.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:50.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:50.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:50.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:50.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:05:50.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.720][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:05:50.722][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.724][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.726][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:05:50.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.731][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.737][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.746][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:05:50.781][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2025-03-01 16:05:50.800][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.805][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.810][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:50.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:50.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.815][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:50.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:50.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.820][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:50.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:50.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.825][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:50.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:50.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.843][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.888][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.893][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.898][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:05:50.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.943][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.945][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.947][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:50.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:50.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.965][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:05:50.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.973][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.979][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.984][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:05:50.985][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.988][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:50.989][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:05:50.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:50.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:50.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:51.004][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:05:51.005][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:05:51.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:51.008][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:51.014][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:51.016][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:51.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:51.018][ef$get] fields variable is a list.
biodb.INFO [2025-03-01 16:05:51.029][biodb::testThat]
biodb.INFO [2025-03-01 16:05:51.030][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-01 16:05:51.032][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:51.033][biodb::testThat]
biodb.DEBUG[2025-03-01 16:05:51.036][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2025-03-01 16:05:51.043][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
biodb.TRACE[2025-03-01 16:05:51.067][cch$loadFileContent] Trying to load 2 files from cache: [2]: "CCDS12227.1, CCDS43240.1".
biodb.INFO [2025-03-01 16:05:51.069][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704" for "ncbi.ccds-c3bf0257a03be04fd46e362b99907704".
biodb.TRACE[2025-03-01 16:05:51.071][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2025-03-01 16:05:51.072][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-01 16:05:51.074][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:05:51.075][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-03-01 16:05:51.076][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-01 16:05:51.077][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-01 16:05:51.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:05:51.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:51.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:51.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:51.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:51.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:51.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:51.103][scheduler$sendRequest] Getting content of get URL request "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.DEBUG[2025-03-01 16:05:51.121][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:05:51.122][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:05:51.124][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-03-01 16:05:59.175][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 does not exist.
biodb.TRACE[2025-03-01 16:05:59.177][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:05:59.178][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:05:59.179][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-03-01 16:05:59.188][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:05:59.189][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:05:59.190][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:05:59.204][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-03-01 16:05:59.211][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 does not exist.
biodb.TRACE[2025-03-01 16:05:59.212][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:05:59.213][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:05:59.215][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-03-01 16:05:59.219][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:05:59.221][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:05:59.223][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:05:59.224][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-03-01 16:05:59.230][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 does not exist.
biodb.TRACE[2025-03-01 16:05:59.231][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:05:59.232][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:05:59.233][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-03-01 16:05:59.237][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:05:59.238][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:05:59.239][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:05:59.242][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-03-01 16:05:59.247][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 does not exist.
biodb.TRACE[2025-03-01 16:05:59.248][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:05:59.250][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:05:59.251][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-03-01 16:05:59.254][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:05:59.256][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:05:59.257][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:05:59.258][rule$waitAsNeeded] Wait 0.945888 second(s).
biodb.TRACE[2025-03-01 16:06:00.225][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-03-01 16:06:00.231][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 does not exist.
biodb.TRACE[2025-03-01 16:06:00.232][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:06:00.234][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:06:00.235][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-03-01 16:06:00.238][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:06:00.240][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:06:00.241][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:06:00.242][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-03-01 16:06:00.248][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 does not exist.
biodb.TRACE[2025-03-01 16:06:00.249][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:06:00.250][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:06:00.252][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-03-01 16:06:00.255][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:06:00.257][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:06:00.258][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:06:00.260][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-03-01 16:06:00.265][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 does not exist.
biodb.TRACE[2025-03-01 16:06:00.266][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:06:00.267][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:06:00.269][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-03-01 16:06:00.272][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:06:00.273][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:06:00.275][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:06:00.276][rule$waitAsNeeded] Wait 0.948616 second(s).
biodb.TRACE[2025-03-01 16:06:01.243][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-03-01 16:06:01.249][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 does not exist.
biodb.TRACE[2025-03-01 16:06:01.250][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:06:01.252][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:06:01.253][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-03-01 16:06:01.257][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:06:01.258][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:06:01.259][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:06:01.267][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-03-01 16:06:01.272][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 does not exist.
biodb.TRACE[2025-03-01 16:06:01.274][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:06:01.275][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:06:01.276][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-03-01 16:06:01.280][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:06:01.281][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:06:01.282][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:06:01.284][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2025-03-01 16:06:01.289][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1 does not exist.
biodb.TRACE[2025-03-01 16:06:01.290][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:06:01.291][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:06:01.293][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.INFO [2025-03-01 16:06:01.296][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:06:01.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:06:01.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:06:01.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:06:01.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:06:01.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:06:01.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:06:01.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:06:01.328][scheduler$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[2025-03-01 16:06:01.343][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:06:01.344][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:06:01.346][rule$waitAsNeeded] Wait 0.896562 second(s).
biodb.TRACE[2025-03-01 16:06:02.259][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-03-01 16:06:02.265][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 does not exist.
biodb.TRACE[2025-03-01 16:06:02.267][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:06:02.268][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:06:02.269][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-03-01 16:06:02.273][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:06:02.274][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:06:02.275][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:06:02.277][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-03-01 16:06:02.282][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 does not exist.
biodb.TRACE[2025-03-01 16:06:02.283][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:06:02.285][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:06:02.286][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-03-01 16:06:02.289][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:06:02.291][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:06:02.292][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:06:02.293][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-03-01 16:06:02.299][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 does not exist.
biodb.TRACE[2025-03-01 16:06:02.300][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:06:02.301][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:06:02.302][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-03-01 16:06:02.306][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:06:02.307][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:06:02.308][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:06:02.309][rule$waitAsNeeded] Wait 0.949698 second(s).
biodb.TRACE[2025-03-01 16:06:03.277][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-03-01 16:06:03.284][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 does not exist.
biodb.TRACE[2025-03-01 16:06:03.291][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:06:03.292][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:06:03.294][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-03-01 16:06:03.297][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:06:03.299][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:06:03.300][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:06:03.301][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-03-01 16:06:03.307][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 does not exist.
biodb.TRACE[2025-03-01 16:06:03.308][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:06:03.309][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:06:03.310][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-03-01 16:06:03.314][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:06:03.315][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:06:03.316][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:06:03.317][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-03-01 16:06:03.323][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 does not exist.
biodb.TRACE[2025-03-01 16:06:03.324][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:06:03.325][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:06:03.326][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-03-01 16:06:03.330][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:06:03.331][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:06:03.332][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:06:03.333][rule$waitAsNeeded] Wait 0.943488 second(s).
biodb.TRACE[2025-03-01 16:06:04.295][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-03-01 16:06:15.347][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 does not exist.
biodb.TRACE[2025-03-01 16:06:15.349][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:06:15.350][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:06:15.352][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-03-01 16:06:26.399][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:06:26.401][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:06:26.402][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:06:26.404][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-03-01 16:06:37.449][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 does not exist.
biodb.TRACE[2025-03-01 16:06:37.451][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:06:37.453][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:06:37.454][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-03-01 16:06:48.547][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:06:48.549][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:06:48.550][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:06:48.552][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-03-01 16:06:59.597][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 does not exist.
biodb.TRACE[2025-03-01 16:06:59.598][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:06:59.600][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:06:59.601][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-03-01 16:07:10.654][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:07:10.656][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:07:10.658][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:07:10.660][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1".
biodb.TRACE[2025-03-01 16:07:21.718][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1 does not exist.
biodb.TRACE[2025-03-01 16:07:21.719][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:07:21.721][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:07:21.722][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1).
biodb.INFO [2025-03-01 16:07:32.778][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS43240.1". Retrying connection to server...
biodb.TRACE[2025-03-01 16:07:32.782][private$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[2025-03-01 16:07:32.785][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-01 16:07:32.787][self$createEntryFromContent] Creating NCBI CCDS entries from 2 content(s).
biodb.DEBUG[2025-03-01 16:07:32.788][self$createEntryFromContent] Parsing 2 NCBI CCDS entries.
biodb.DEBUG[2025-03-01 16:07:32.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:07:32.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:32.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:32.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:32.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:32.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:32.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:07:32.804][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:32.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:32.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:32.809][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:32.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:32.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:32.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:32.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:32.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:07:32.819][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:07:32.820][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:32.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:32.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:32.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:32.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:32.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:07:32.833][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:32.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:32.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:32.838][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:32.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:32.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:32.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:32.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:32.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:32.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:32.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:32.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:32.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:32.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:32.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:32.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:32.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:32.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:32.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:32.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:32.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:32.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:32.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:32.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:32.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:32.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:32.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:32.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:32.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:32.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:32.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:32.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:32.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:32.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:32.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:32.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:32.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:32.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:32.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:32.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:07:32.904][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2025-03-01 16:07:32.905][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-01 16:07:32.926][biodb::testThat]
biodb.INFO [2025-03-01 16:07:32.928][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-01 16:07:32.929][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:07:32.930][biodb::testThat]
biodb.INFO [2025-03-01 16:07:32.939][biodb::testThat]
biodb.INFO [2025-03-01 16:07:32.940][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-01 16:07:32.941][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:07:32.943][biodb::testThat]
biodb.WARN [2025-03-01 16:07:32.960][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-03-01 16:07:32.987][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-03-01 16:07:32.999][biodb::testThat]
biodb.INFO [2025-03-01 16:07:33.000][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-01 16:07:33.001][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:07:33.002][biodb::testThat]
biodb.INFO [2025-03-01 16:07:33.157][biodb::testThat]
biodb.INFO [2025-03-01 16:07:33.158][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-01 16:07:33.159][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:07:33.161][biodb::testThat]
biodb.INFO [2025-03-01 16:07:33.216][biodb::testThat]
biodb.INFO [2025-03-01 16:07:33.217][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-01 16:07:33.219][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:07:33.220][biodb::testThat]
biodb.INFO [2025-03-01 16:07:33.230][biodb::testThat]
biodb.INFO [2025-03-01 16:07:33.231][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-01 16:07:33.232][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:07:33.233][biodb::testThat]
biodb.DEBUG[2025-03-01 16:07:33.238][function(conn, opt)] Trying to download "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.DEBUG[2025-03-01 16:07:44.289][getUrlContent] Use base::url() for downloading content of URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1.
biodb.INFO [2025-03-01 16:07:55.562][biodb::testThat]
biodb.INFO [2025-03-01 16:07:55.563][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-01 16:07:55.565][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:07:55.566][biodb::testThat]
biodb.INFO [2025-03-01 16:07:55.574][bdb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-01 16:07:55.575][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.ccds from the request scheduler
biodb.INFO [2025-03-01 16:07:55.577][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-03-01 16:07:55.578][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-01 16:07:55.579][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:55.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:55.581][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.583][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-01 16:07:55.607][biodb::testContext]
biodb.INFO [2025-03-01 16:07:55.609][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:07:55.610][biodb::testContext] Test context - Gene long tests
biodb.INFO [2025-03-01 16:07:55.611][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:07:55.613][biodb::testContext]
biodb.INFO [2025-03-01 16:07:55.616][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:07:55.618][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-01 16:07:55.624][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:07:55.625][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-01 16:07:55.626][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-01 16:07:55.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.631][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-01 16:07:55.632][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-01 16:07:55.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.636][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-01 16:07:55.637][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-01 16:07:55.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.642][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-01 16:07:55.643][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-01 16:07:55.644][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-01 16:07:55.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.648][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-01 16:07:55.650][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-01 16:07:55.651][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-01 16:07:55.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.654][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[2025-03-01 16:07:55.655][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-01 16:07:55.656][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-01 16:07:55.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.661][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-01 16:07:55.662][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-01 16:07:55.663][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-01 16:07:55.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.668][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-01 16:07:55.669][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-01 16:07:55.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.673][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-01 16:07:55.675][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-01 16:07:55.676][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-01 16:07:55.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.680][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:07:55.682][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-01 16:07:55.683][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-01 16:07:55.684][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-01 16:07:55.686][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-01 16:07:55.687][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-01 16:07:55.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.692][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-01 16:07:55.694][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-01 16:07:55.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.699][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-01 16:07:55.700][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-01 16:07:55.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.705][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-01 16:07:55.706][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-01 16:07:55.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.711][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-01 16:07:55.713][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-01 16:07:55.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.718][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-01 16:07:55.719][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-01 16:07:55.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.723][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[2025-03-01 16:07:55.724][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:07:55.726][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-01 16:07:55.729][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-01 16:07:55.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.734][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-01 16:07:55.736][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-01 16:07:55.737][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-01 16:07:55.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.741][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[2025-03-01 16:07:55.742][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-01 16:07:55.745][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:55.746][self$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[2025-03-01 16:07:55.747][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.749][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:07:55.750][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.752][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:07:55.753][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:55.754][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:07:55.756][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:07:55.757][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:07:55.759][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.760][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-01 16:07:55.761][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:07:55.763][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:55.764][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.765][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:07:55.765][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:07:55.765][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:07:55.765][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:07:55.765][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:07:55.767][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:07:55.768][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:55.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:55.771][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:07:55.772][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:55.773][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:55.775][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:07:55.776][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:55.777][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:07:55.779][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:07:55.780][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:55.781][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:55.783][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-01 16:07:55.785][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:55.786][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:07:55.788][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.789][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:07:55.791][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.792][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:07:55.793][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:55.795][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:07:55.796][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:07:55.797][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:07:55.799][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.800][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-01 16:07:55.801][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:07:55.803][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:55.804][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.806][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:07:55.806][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:07:55.806][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:07:55.806][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:07:55.806][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:07:55.807][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:07:55.808][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:55.809][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:55.811][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:07:55.812][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:55.813][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:55.815][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:07:55.816][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:55.818][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:07:55.819][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:07:55.820][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:55.822][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:55.823][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-01 16:07:55.825][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.827][self$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[2025-03-01 16:07:55.828][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.829][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:07:55.831][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.832][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:07:55.833][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:55.835][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:07:55.836][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:07:55.838][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:07:55.839][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:55.840][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-01 16:07:55.842][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:07:55.843][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:55.844][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.846][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:55.848][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:07:55.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:55.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:55.852][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:07:55.854][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:55.855][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:55.856][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:07:55.858][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:55.859][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:07:55.860][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:07:55.862][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:55.863][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:55.865][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-01 16:07:55.867][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.868][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:07:55.870][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.871][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:07:55.873][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.874][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:07:55.875][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:55.877][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:07:55.878][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:07:55.880][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:07:55.881][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:55.882][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-01 16:07:55.884][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:07:55.885][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:55.886][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:55.888][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:55.889][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:07:55.890][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:55.892][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:55.893][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:07:55.894][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:55.895][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:55.897][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:07:55.898][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:55.899][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:07:55.901][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:07:55.902][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:55.903][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:55.905][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:07:55.906][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.945][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[2025-03-01 16:07:55.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:55.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:55.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:55.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:55.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:55.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:56.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.007][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[2025-03-01 16:07:56.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.013][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[2025-03-01 16:07:56.014][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-01 16:07:56.016][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-01 16:07:56.018][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-01 16:07:56.020][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-01 16:07:56.021][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-01 16:07:56.023][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-01 16:07:56.025][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-01 16:07:56.027][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-01 16:07:56.029][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-01 16:07:56.030][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-01 16:07:56.032][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-01 16:07:56.035][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-01 16:07:56.037][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-01 16:07:56.040][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-01 16:07:56.043][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:07:56.044][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:07:56.046][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-01 16:07:56.048][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-01 16:07:56.050][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-01 16:07:56.051][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-01 16:07:56.053][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-01 16:07:56.055][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-01 16:07:56.057][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-01 16:07:56.059][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-01 16:07:56.060][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-01 16:07:56.062][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-01 16:07:56.064][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-01 16:07:56.066][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-01 16:07:56.067][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-01 16:07:56.069][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-01 16:07:56.071][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-01 16:07:56.073][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-01 16:07:56.075][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-01 16:07:56.076][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-01 16:07:56.078][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-01 16:07:56.080][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-01 16:07:56.082][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-01 16:07:56.084][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-01 16:07:56.085][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-01 16:07:56.087][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-01 16:07:56.089][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-01 16:07:56.091][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-01 16:07:56.093][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-01 16:07:56.094][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-01 16:07:56.096][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-01 16:07:56.098][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:07:56.100][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-01 16:07:56.101][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-01 16:07:56.103][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-01 16:07:56.105][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-01 16:07:56.107][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-01 16:07:56.114][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-01 16:07:56.116][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-01 16:07:56.118][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-01 16:07:56.119][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-01 16:07:56.121][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-01 16:07:56.122][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-01 16:07:56.124][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-01 16:07:56.125][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-01 16:07:56.127][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-01 16:07:56.128][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-01 16:07:56.130][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-01 16:07:56.132][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-01 16:07:56.133][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-01 16:07:56.135][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-01 16:07:56.136][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-01 16:07:56.138][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-01 16:07:56.139][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-01 16:07:56.141][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-01 16:07:56.142][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-01 16:07:56.144][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-01 16:07:56.146][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-01 16:07:56.147][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-01 16:07:56.149][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-01 16:07:56.150][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-01 16:07:56.152][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-01 16:07:56.153][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-01 16:07:56.155][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-01 16:07:56.157][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-01 16:07:56.158][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-01 16:07:56.160][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-01 16:07:56.161][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-01 16:07:56.163][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-01 16:07:56.165][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-01 16:07:56.167][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:07:56.168][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:07:56.169][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.171][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:56.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.180][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[2025-03-01 16:07:56.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:56.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.195][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[2025-03-01 16:07:56.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.202][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[2025-03-01 16:07:56.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:56.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:56.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:56.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:56.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.240][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[2025-03-01 16:07:56.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:56.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.255][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[2025-03-01 16:07:56.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:56.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:56.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:56.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.285][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[2025-03-01 16:07:56.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:56.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:07:56.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:56.303][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-03-01 16:07:56.305][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-03-01 16:07:56.307][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.308][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-03-01 16:07:56.310][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.311][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:07:56.312][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.313][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:07:56.314][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.315][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:07:56.317][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-03-01 16:07:56.318][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:07:56.319][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.320][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-03-01 16:07:56.321][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:07:56.323][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-03-01 16:07:56.323][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-03-01 16:07:56.324][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:56.325][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:56.326][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:07:56.327][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:56.328][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:56.330][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:07:56.331][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:56.332][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:56.333][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:07:56.334][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-03-01 16:07:56.334][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-03-01 16:07:56.335][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:07:56.336][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:07:56.338][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.339][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:56.340][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-03-01 16:07:56.342][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.343][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-03-01 16:07:56.344][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.346][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:07:56.347][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.348][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:07:56.349][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.350][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:07:56.352][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-01 16:07:56.353][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:07:56.354][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.355][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-03-01 16:07:56.356][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:07:56.358][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-03-01 16:07:56.358][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-03-01 16:07:56.358][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-03-01 16:07:56.358][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-03-01 16:07:56.358][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-03-01 16:07:56.358][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-03-01 16:07:56.359][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:56.360][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:07:56.361][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:07:56.362][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:56.363][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:56.365][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:07:56.366][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:56.367][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:56.368][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:07:56.369][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-03-01 16:07:56.369][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-03-01 16:07:56.370][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:07:56.371][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:07:56.372][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.374][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:56.375][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-03-01 16:07:56.377][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:56.378][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-03-01 16:07:56.380][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.381][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:07:56.382][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.383][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:07:56.384][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.385][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:07:56.387][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-01 16:07:56.388][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:07:56.389][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.390][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-03-01 16:07:56.391][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:07:56.393][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-03-01 16:07:56.393][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:07:56.393][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:07:56.393][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:07:56.393][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:07:56.393][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:07:56.393][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:07:56.393][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:07:56.393][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:07:56.393][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:07:56.393][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-03-01 16:07:56.393][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:07:56.393][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:07:56.393][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:07:56.394][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:56.395][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:07:56.395][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:07:56.395][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:07:56.396][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-03-01 16:07:56.398][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:56.399][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:56.400][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:07:56.401][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:56.402][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:56.403][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:07:56.404][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-03-01 16:07:56.404][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-03-01 16:07:56.404][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-03-01 16:07:56.405][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:07:56.407][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:07:56.408][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.409][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-03-01 16:07:56.410][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-03-01 16:07:56.412][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.414][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-03-01 16:07:56.415][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.416][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:07:56.417][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.418][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:07:56.419][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.421][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:07:56.422][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-01 16:07:56.423][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:07:56.424][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.425][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-03-01 16:07:56.427][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:07:56.428][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-03-01 16:07:56.428][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-03-01 16:07:56.429][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:07:56.430][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:07:56.431][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-03-01 16:07:56.432][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:56.433][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:56.435][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:07:56.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:07:56.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:07:56.438][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:07:56.439][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-03-01 16:07:56.439][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-03-01 16:07:56.439][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-03-01 16:07:56.440][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:07:56.442][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:07:56.443][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:07:56.444][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-03-01 16:07:56.445][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-03-01 16:07:56.447][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:07:56.449][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:07:56.451][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-03-01 16:07:56.452][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:07:56.454][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-03-01 16:07:56.461][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2025-03-01 16:07:56.462][super$initialize] Register connector ncbi.gene with the request scheduler
biodb.DEBUG[2025-03-01 16:07:56.464][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.gene.
biodb.DEBUG[2025-03-01 16:07:56.465][private$addConnectorRules] Create new rule for URL "www.ncbi.nlm.nih.gov" of connector "ncbi.gene".
biodb.DEBUG[2025-03-01 16:07:56.467][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:07:56.468][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:07:56.470][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.gene".
biodb.DEBUG[2025-03-01 16:07:56.471][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:07:56.472][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:07:56.527][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2025-03-01 16:07:56.533][biodb::testThat]
biodb.INFO [2025-03-01 16:07:56.535][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-01 16:07:56.536][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:07:56.537][biodb::testThat]
biodb.TRACE[2025-03-01 16:07:56.563][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2025-03-01 16:07:56.564][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:07:56.568][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-03-01 16:07:56.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:07:56.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.582][FUN] Functions in observer BiodbConfig: [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[2025-03-01 16:07:56.595][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:56.597][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:56.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.607][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:56.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:56.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.614][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:07:56.615][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:07:56.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.618][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.620][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:07:56.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:07:56.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.625][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:07:56.626][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:07:56.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.628][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.631][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:07:56.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:07:56.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.636][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:07:56.637][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:07:56.638][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.639][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.642][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:07:56.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:07:56.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.647][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:07:56.648][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:07:56.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.650][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.653][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:07:56.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:07:56.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.658][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:07:56.659][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:07:56.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.661][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.665][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:07:56.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:07:56.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.674][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:56.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:56.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.679][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:07:56.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:07:56.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.684][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:07:56.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:07:56.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:56.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:56.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.693][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:07:56.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:07:56.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:56.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:56.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:56.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:56.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:56.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:56.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:56.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:56.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:56.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:56.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:07:56.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:07:56.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:07:56.727][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2025-03-01 16:07:56.730][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:07:56.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:07:56.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.735][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:07:56.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:07:56.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.740][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:56.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:56.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.745][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:56.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:56.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:07:56.749][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:56.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:07:56.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:07:56.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:07:56.754][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-03-01 16:07:56.779][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-03-01 16:07:56.780][initialize] Register connector ncbi.ccds with the request scheduler
biodb.DEBUG[2025-03-01 16:07:56.782][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.ccds.
biodb.DEBUG[2025-03-01 16:07:56.796][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2025-03-01 16:07:56.798][self$recomputeFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:07:56.799][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2025-03-01 16:07:56.809][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:07:56.811][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:07:56.812][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2025-03-01 16:07:56.813][self$recomputeFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:07:56.815][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2025-03-01 16:07:56.816][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:07:56.817][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:07:56.828][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2025-03-01 16:07:56.830][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2025-03-01 16:07:56.832][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-01 16:07:56.835][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS14416.1".
biodb.TRACE[2025-03-01 16:07:56.837][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-01 16:07:56.838][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-01 16:07:56.840][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:07:56.841][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-03-01 16:07:56.842][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-01 16:07:56.843][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-01 16:07:56.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:07:56.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:07:56.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:07:56.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:07:56.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:07:56.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:07:56.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:07:56.860][scheduler$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[2025-03-01 16:07:56.863][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:07:56.864][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:07:56.865][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-03-01 16:08:07.914][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 does not exist.
biodb.TRACE[2025-03-01 16:08:07.916][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:08:07.917][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:08:07.918][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-03-01 16:08:18.966][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:08:18.968][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:08:18.969][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:08:18.970][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-03-01 16:08:24.162][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 does not exist.
biodb.TRACE[2025-03-01 16:08:24.164][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:08:24.165][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:08:24.166][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-03-01 16:08:24.170][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:08:24.171][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:08:24.172][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:08:24.174][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-03-01 16:08:24.179][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 does not exist.
biodb.TRACE[2025-03-01 16:08:24.180][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:08:24.181][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:08:24.183][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-03-01 16:08:24.186][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:08:24.187][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:08:24.188][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:08:24.190][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-03-01 16:08:24.195][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 does not exist.
biodb.TRACE[2025-03-01 16:08:24.196][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:08:24.198][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:08:24.199][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-03-01 16:08:24.202][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:08:24.204][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:08:24.205][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:08:24.206][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-03-01 16:08:24.212][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 does not exist.
biodb.TRACE[2025-03-01 16:08:24.213][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:08:24.214][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:08:24.215][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-03-01 16:08:24.219][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:08:24.220][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:08:24.221][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:08:24.223][rule$waitAsNeeded] Wait 0.950977 second(s).
biodb.TRACE[2025-03-01 16:08:25.183][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-03-01 16:08:25.190][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 does not exist.
biodb.TRACE[2025-03-01 16:08:25.191][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:08:25.192][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:08:25.194][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-03-01 16:08:25.197][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:08:25.198][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:08:25.199][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:08:25.201][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-03-01 16:08:25.206][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 does not exist.
biodb.TRACE[2025-03-01 16:08:25.207][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:08:25.209][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:08:25.210][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-03-01 16:08:25.213][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:08:25.214][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:08:25.215][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:08:25.217][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-03-01 16:08:25.222][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 does not exist.
biodb.TRACE[2025-03-01 16:08:25.223][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:08:25.224][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:08:25.226][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-03-01 16:08:25.229][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:08:25.230][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:08:25.231][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:08:25.233][rule$waitAsNeeded] Wait 0.949794 second(s).
biodb.TRACE[2025-03-01 16:08:26.201][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-03-01 16:08:26.208][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 does not exist.
biodb.TRACE[2025-03-01 16:08:26.209][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:08:26.210][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:08:26.212][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-03-01 16:08:26.215][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:08:26.216][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:08:26.217][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:08:26.219][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2025-03-01 16:08:26.224][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1 does not exist.
biodb.TRACE[2025-03-01 16:08:26.225][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:08:26.227][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:08:26.228][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.INFO [2025-03-01 16:08:26.231][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:08:26.234][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS14416.1.html"
biodb.DEBUG[2025-03-01 16:08:26.236][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-01 16:08:26.238][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:08:26.239][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-03-01 16:08:26.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:08:26.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:08:26.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:08:26.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:08:26.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:08:26.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:08:26.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:08:26.255][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.260][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:08:26.294][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-03-01 16:08:26.295][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.TRACE[2025-03-01 16:08:26.296][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:08:26.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:08:26.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.307][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:08:26.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:08:26.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.312][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:08:26.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:08:26.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.316][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:08:26.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:08:26.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.332][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:08:26.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:08:26.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.372][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:08:26.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:08:26.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.377][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:08:26.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:08:26.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.381][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:08:26.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:08:26.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.420][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.421][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.424][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.439][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:08:26.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:08:26.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.444][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:08:26.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:08:26.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.449][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:08:26.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:08:26.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.453][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:08:26.455][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:08:26.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.457][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.458][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:08:26.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:08:26.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.472][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:08:26.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:08:26.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.477][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:08:26.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:08:26.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.482][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:08:26.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:08:26.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.487][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:08:26.488][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:08:26.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.490][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.491][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:08:26.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:08:26.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.505][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.510][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.515][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.520][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.521][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.523][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.524][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.539][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.544][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.548][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.553][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.555][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.557][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.558][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.572][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:08:26.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:08:26.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.577][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:08:26.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:08:26.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.582][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:08:26.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:08:26.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.587][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:08:26.588][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:08:26.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.590][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.591][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:08:26.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:08:26.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.605][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:08:26.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:08:26.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.610][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:08:26.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:08:26.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.614][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:08:26.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:08:26.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.619][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:08:26.620][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:08:26.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.623][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.624][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:08:26.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:08:26.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.637][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:08:26.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:08:26.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.642][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:08:26.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:08:26.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.654][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:08:26.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:08:26.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.658][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:08:26.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:08:26.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.663][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.668][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.673][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:08:26.678][private$computeField] Compute value for field "aa.seq".
biodb.TRACE[2025-03-01 16:08:26.679][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:08:26.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:08:26.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.684][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:08:26.685][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:08:26.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.687][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.688][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:08:26.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:08:26.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.728][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:08:26.730][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:08:26.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.732][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.738][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.740][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.742][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.748][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:08:26.749][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:08:26.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.752][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.758][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:08:26.759][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:08:26.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.761][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.767][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:08:26.769][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:08:26.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.771][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.777][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.778][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.780][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.786][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.788][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.795][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.825][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-3002-content.xml".
biodb.DEBUG[2025-03-01 16:08:26.827][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:08:26.829][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-03-01 16:08:26.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:08:26.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:08:26.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:08:26.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:08:26.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:08:26.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:08:26.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:08:26.855][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.856][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.859][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.866][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:08:26.867][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:08:26.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.869][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.871][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:08:26.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:08:26.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.876][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:08:26.877][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:08:26.879][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.880][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.882][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:08:26.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:08:26.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.887][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:08:26.888][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:08:26.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.890][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.892][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:08:26.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:08:26.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.897][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:08:26.899][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:08:26.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.901][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.903][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:08:26.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:08:26.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.908][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.909][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.911][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.914][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:08:26.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.922][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.927][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:08:26.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:08:26.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.932][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:08:26.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:08:26.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.942][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:08:26.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:08:26.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:08:26.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:08:26.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:08:26.976][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3002.
biodb.TRACE[2025-03-01 16:08:26.978][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:08:26.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:08:26.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.983][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:08:26.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:08:26.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.988][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.992][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:26.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:08:26.997][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:26.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:08:27.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:08:27.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:08:27.002][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-03-01 16:08:27.003][private$loadEntries] Creating entries from ids [1]: "CCDS9633.1".
biodb.DEBUG[2025-03-01 16:08:27.041][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-01 16:08:27.056][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS9633.1".
biodb.TRACE[2025-03-01 16:08:27.058][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-01 16:08:27.059][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-01 16:08:27.060][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:08:27.062][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-03-01 16:08:27.063][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-01 16:08:27.064][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-01 16:08:27.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:08:27.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:08:27.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:08:27.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:08:27.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:08:27.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:08:27.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:08:27.089][scheduler$sendRequest] Getting content of get URL request "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.DEBUG[2025-03-01 16:08:27.092][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:08:27.094][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:08:27.095][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-03-01 16:08:27.101][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 does not exist.
biodb.TRACE[2025-03-01 16:08:27.102][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:08:27.103][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:08:27.104][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-03-01 16:08:27.108][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:08:27.109][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:08:27.110][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:08:27.111][rule$waitAsNeeded] Wait 0.0892379 second(s).
biodb.TRACE[2025-03-01 16:08:27.203][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-03-01 16:08:27.211][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 does not exist.
biodb.TRACE[2025-03-01 16:08:27.212][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:08:27.213][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:08:27.214][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-03-01 16:08:27.218][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:08:27.219][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:08:27.220][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:08:27.222][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-03-01 16:08:27.227][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 does not exist.
biodb.TRACE[2025-03-01 16:08:27.228][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:08:27.229][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:08:27.231][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-03-01 16:08:27.234][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:08:27.235][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:08:27.236][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:08:27.238][rule$waitAsNeeded] Wait 0.857413 second(s).
biodb.TRACE[2025-03-01 16:08:28.111][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-03-01 16:08:39.173][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 does not exist.
biodb.TRACE[2025-03-01 16:08:39.174][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:08:39.176][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:08:39.178][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-03-01 16:08:50.230][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:08:50.231][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:08:50.233][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:08:50.235][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-03-01 16:09:01.285][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 does not exist.
biodb.TRACE[2025-03-01 16:09:01.286][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:09:01.288][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:09:01.289][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-03-01 16:09:12.343][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:09:12.344][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:09:12.345][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:09:12.347][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-03-01 16:09:23.397][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 does not exist.
biodb.TRACE[2025-03-01 16:09:23.399][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:09:23.401][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:09:23.402][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-03-01 16:09:34.482][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:09:34.484][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:09:34.485][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:09:34.487][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-03-01 16:09:45.549][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 does not exist.
biodb.TRACE[2025-03-01 16:09:45.550][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:09:45.552][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:09:45.554][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-03-01 16:09:56.609][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:09:56.610][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:09:56.612][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:09:56.614][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-03-01 16:09:59.393][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 does not exist.
biodb.TRACE[2025-03-01 16:09:59.394][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:09:59.396][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:09:59.398][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-03-01 16:09:59.402][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:09:59.403][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:09:59.404][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:09:59.406][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-03-01 16:09:59.411][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 does not exist.
biodb.TRACE[2025-03-01 16:09:59.412][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:09:59.414][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:09:59.415][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-03-01 16:09:59.418][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:09:59.419][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:09:59.421][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:09:59.422][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1".
biodb.TRACE[2025-03-01 16:09:59.428][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1 does not exist.
biodb.TRACE[2025-03-01 16:09:59.429][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:09:59.430][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:09:59.431][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1).
biodb.INFO [2025-03-01 16:09:59.435][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS9633.1". Retrying connection to server...
biodb.TRACE[2025-03-01 16:09:59.447][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS9633.1.html"
biodb.DEBUG[2025-03-01 16:09:59.450][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-01 16:09:59.451][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:09:59.453][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-03-01 16:09:59.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:09:59.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:09:59.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:09:59.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:09:59.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:09:59.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:09:59.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:09:59.469][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.474][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:09:59.515][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-03-01 16:09:59.516][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.TRACE[2025-03-01 16:09:59.525][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:09:59.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:09:59.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.530][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:09:59.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:09:59.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.535][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:09:59.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:09:59.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.539][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:09:59.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:09:59.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.555][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:09:59.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:09:59.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.596][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:09:59.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:09:59.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.601][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:09:59.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:09:59.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.606][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:09:59.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:09:59.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.646][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.648][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.650][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.665][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:09:59.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:09:59.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.670][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:09:59.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:09:59.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.675][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:09:59.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:09:59.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.680][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:09:59.681][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:09:59.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.683][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.684][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:09:59.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:09:59.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.699][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:09:59.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:09:59.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.704][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:09:59.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:09:59.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.708][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:09:59.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:09:59.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.713][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:09:59.714][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:09:59.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.717][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.718][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:09:59.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:09:59.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.732][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:09:59.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:09:59.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.737][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:09:59.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:09:59.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.742][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:09:59.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:09:59.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.746][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:09:59.748][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:09:59.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.750][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.751][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:09:59.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:09:59.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.765][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.770][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.775][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.779][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.781][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.783][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.784][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.799][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:09:59.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:09:59.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.803][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:09:59.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:09:59.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.808][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:09:59.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:09:59.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.813][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:09:59.814][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:09:59.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.817][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.818][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:09:59.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:09:59.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.832][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:09:59.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:09:59.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.837][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:09:59.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:09:59.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.842][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:09:59.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:09:59.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.847][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:09:59.848][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:09:59.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.850][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.852][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:09:59.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:09:59.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.866][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:09:59.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:09:59.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.871][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:09:59.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:09:59.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.876][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:09:59.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:09:59.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.880][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:09:59.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:09:59.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.885][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.890][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.895][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:09:59.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:09:59.900][private$computeField] Compute value for field "aa.seq".
biodb.TRACE[2025-03-01 16:09:59.901][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:09:59.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:09:59.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.906][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:09:59.907][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:09:59.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.909][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.910][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:09:59.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:09:59.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.950][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:09:59.952][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:09:59.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.954][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.961][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:09:59.962][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:09:59.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.964][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.971][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:09:59.972][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:09:59.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.974][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.987][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:09:59.988][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:09:59.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:09:59.990][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:09:59.997][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:09:59.998][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:09:59.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.000][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.007][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.008][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.010][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.017][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.018][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.020][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.057][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-3627-content.xml".
biodb.DEBUG[2025-03-01 16:10:00.059][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:10:00.061][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-03-01 16:10:00.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:10:00.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:10:00.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:10:00.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:10:00.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:10:00.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:10:00.075][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.TRACE[2025-03-01 16:10:00.099][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.100][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.103][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.111][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:00.112][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:00.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.114][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.118][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:00.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:00.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.123][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:00.124][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:00.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.126][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.129][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:00.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:00.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.134][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:00.136][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:00.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.141][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:00.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:00.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.146][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:00.147][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:00.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.150][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.153][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:00.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:00.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.158][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.159][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.162][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.167][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.175][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.180][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.185][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.195][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:10:00.228][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3627.
biodb.TRACE[2025-03-01 16:10:00.231][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:00.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:00.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.236][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:00.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:00.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.240][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.245][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.250][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:10:00.255][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-03-01 16:10:00.256][private$loadEntries] Creating entries from ids [1]: "CCDS43240.1".
biodb.DEBUG[2025-03-01 16:10:00.257][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-01 16:10:00.259][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS43240.1".
biodb.TRACE[2025-03-01 16:10:00.261][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:10:00.263][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS43240.1.html".
biodb.DEBUG[2025-03-01 16:10:00.264][conn$getEntryContent] 1 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:10:00.266][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:10:00.267][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-03-01 16:10:00.269][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:10:00.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:10:00.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:10:00.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:10:00.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:10:00.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:10:00.281][FUN] Functions in observer BiodbConfig: [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[2025-03-01 16:10:00.283][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.288][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:10:00.322][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-03-01 16:10:00.323][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.TRACE[2025-03-01 16:10:00.324][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:10:00.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:10:00.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.329][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:10:00.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:10:00.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.334][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:10:00.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:10:00.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.339][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:10:00.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:10:00.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.356][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.397][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.402][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.407][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.445][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.446][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.448][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.464][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:00.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:00.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.469][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:00.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:00.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.474][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:00.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:00.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.479][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:00.480][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:00.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.482][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.483][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:00.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:00.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.498][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:00.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:00.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.503][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:00.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:00.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.508][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:00.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:00.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.513][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:00.514][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:00.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.516][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.517][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:00.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:00.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.532][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.537][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.542][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.547][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.548][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.550][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.551][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.572][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.577][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.581][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.586][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.587][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.590][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.591][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.605][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:00.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:00.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.610][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:00.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:00.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.615][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:00.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:00.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.620][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:00.622][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:00.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.624][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.625][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:00.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:00.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.639][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:00.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:00.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.644][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:10:00.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:00.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.649][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:10:00.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:00.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.654][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:00.655][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:00.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.658][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.659][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:00.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:00.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.673][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:10:00.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:00.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.678][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:00.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:00.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.683][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:00.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:00.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.688][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:00.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:00.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.693][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.698][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.702][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:10:00.707][private$computeField] Compute value for field "aa.seq".
biodb.TRACE[2025-03-01 16:10:00.709][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:00.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:00.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.713][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:10:00.715][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:00.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.717][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.718][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:10:00.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:00.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.758][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:00.760][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:00.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.762][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.768][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.770][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.772][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.778][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:00.780][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:00.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.782][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.788][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:00.790][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:00.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.792][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.799][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:10:00.800][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:00.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.802][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.809][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.810][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.813][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.819][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.821][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.823][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.852][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-4316-content.xml".
biodb.DEBUG[2025-03-01 16:10:00.854][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:10:00.856][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-03-01 16:10:00.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:10:00.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:10:00.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:10:00.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:10:00.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:10:00.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:10:00.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:10:00.887][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.888][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.890][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.891][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.898][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:00.900][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:00.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.905][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:00.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:00.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.910][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:00.911][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:00.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.913][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.916][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:00.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:00.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.921][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:00.922][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:00.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.924][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.927][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:00.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:00.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.932][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:00.933][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:00.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.935][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.938][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:00.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:00.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.943][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.944][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.946][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.951][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:00.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.958][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:00.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.962][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.967][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.977][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:00.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:00.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:00.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:00.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:00.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:01.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:01.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:01.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:01.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:01.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:01.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:01.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:01.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:10:01.010][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 4316.
biodb.TRACE[2025-03-01 16:10:01.013][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:01.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:01.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:01.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:01.017][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:01.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:01.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:01.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:01.022][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:01.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:01.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:01.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:01.027][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:01.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:01.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:01.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:01.032][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:01.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:01.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:01.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:10:01.037][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-03-01 16:10:01.038][private$loadEntries] Creating entries from ids [1]: "CCDS8317.1".
biodb.DEBUG[2025-03-01 16:10:01.039][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-01 16:10:01.041][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS8317.1".
biodb.TRACE[2025-03-01 16:10:01.043][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-01 16:10:01.044][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-01 16:10:01.045][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:10:01.047][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-03-01 16:10:01.048][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-01 16:10:01.049][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-01 16:10:01.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:10:01.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:10:01.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:10:01.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:10:01.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:10:01.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:10:01.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:10:01.066][scheduler$sendRequest] Getting content of get URL request "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.DEBUG[2025-03-01 16:10:01.069][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:01.071][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:10:01.072][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-03-01 16:10:01.082][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 does not exist.
biodb.TRACE[2025-03-01 16:10:01.083][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:01.085][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:01.086][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-03-01 16:10:01.091][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:10:01.092][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:01.093][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:10:01.095][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-03-01 16:10:01.101][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 does not exist.
biodb.TRACE[2025-03-01 16:10:01.102][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:01.103][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:01.105][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-03-01 16:10:01.108][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:10:01.109][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:01.111][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:10:01.119][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-03-01 16:10:01.124][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 does not exist.
biodb.TRACE[2025-03-01 16:10:01.126][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:01.127][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:01.128][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-03-01 16:10:01.132][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:10:01.133][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:01.134][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:10:01.135][rule$waitAsNeeded] Wait 0.936734 second(s).
biodb.TRACE[2025-03-01 16:10:02.090][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-03-01 16:10:02.097][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 does not exist.
biodb.TRACE[2025-03-01 16:10:02.098][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:02.099][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:02.101][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-03-01 16:10:02.104][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:10:02.105][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:02.106][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:10:02.108][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-03-01 16:10:02.114][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 does not exist.
biodb.TRACE[2025-03-01 16:10:02.115][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:02.116][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:02.117][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-03-01 16:10:02.120][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:10:02.122][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:02.123][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:10:02.124][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-03-01 16:10:02.130][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 does not exist.
biodb.TRACE[2025-03-01 16:10:02.131][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:02.132][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:02.133][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-03-01 16:10:02.246][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:10:02.248][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:02.249][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:10:02.251][rule$waitAsNeeded] Wait 0.838255 second(s).
biodb.TRACE[2025-03-01 16:10:03.107][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-03-01 16:10:03.114][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 does not exist.
biodb.TRACE[2025-03-01 16:10:03.115][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:03.116][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:03.118][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-03-01 16:10:03.121][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:10:03.123][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:03.124][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:10:03.125][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-03-01 16:10:03.131][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 does not exist.
biodb.TRACE[2025-03-01 16:10:03.132][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:03.133][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:03.134][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-03-01 16:10:03.138][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:10:03.139][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:03.140][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:10:03.141][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-03-01 16:10:03.147][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 does not exist.
biodb.TRACE[2025-03-01 16:10:03.148][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:03.149][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:03.150][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-03-01 16:10:03.154][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:10:03.155][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:03.156][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:10:03.157][rule$waitAsNeeded] Wait 0.949449 second(s).
biodb.TRACE[2025-03-01 16:10:04.126][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1".
biodb.TRACE[2025-03-01 16:10:13.720][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1 does not exist.
biodb.TRACE[2025-03-01 16:10:13.722][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:13.723][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:13.725][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS8317.1).
biodb.INFO [2025-03-01 16:10:13.728][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:10:13.731][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS8317.1.html"
biodb.DEBUG[2025-03-01 16:10:13.734][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-01 16:10:13.735][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:10:13.737][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-03-01 16:10:13.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:10:13.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:10:13.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:10:13.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:10:13.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:10:13.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:10:13.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:10:13.753][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:13.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:13.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.757][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:13.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:13.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:10:13.790][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-03-01 16:10:13.792][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.TRACE[2025-03-01 16:10:13.793][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:10:13.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:10:13.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.798][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:10:13.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:10:13.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.802][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:10:13.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:10:13.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.807][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:10:13.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:10:13.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.823][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:13.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:13.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.863][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:13.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:13.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.868][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:13.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:13.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.872][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:13.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:13.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.910][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.911][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.914][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:13.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:13.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.929][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:13.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:13.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.934][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:13.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:13.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.938][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:13.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:13.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.943][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:13.944][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:13.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.947][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.948][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:13.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:13.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.962][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:13.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:13.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.967][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:13.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:13.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.971][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:13.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:13.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.976][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:13.977][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:13.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.980][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.981][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:13.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:13.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.995][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:13.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:13.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:13.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:13.999][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:14.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:14.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.004][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:14.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:14.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.009][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:14.010][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:14.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.012][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.013][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:14.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:14.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.028][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.033][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.037][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.042][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.043][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.046][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.047][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.061][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:14.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:14.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.066][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:14.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:14.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.071][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:14.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:14.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.076][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:14.077][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:14.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.079][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.081][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:14.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:14.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.095][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:14.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:14.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.100][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:10:14.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:14.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.105][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:10:14.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:14.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.110][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:14.111][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:14.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.113][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.115][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:14.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:14.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.129][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:10:14.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:14.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.161][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:14.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:14.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.166][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:14.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:14.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.171][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:14.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:14.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.176][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.180][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.185][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:10:14.190][private$computeField] Compute value for field "aa.seq".
biodb.TRACE[2025-03-01 16:10:14.191][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:14.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:14.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.196][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:10:14.197][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:14.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.199][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.200][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:10:14.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:14.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.241][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:14.242][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:14.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.244][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.251][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:14.252][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:14.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.254][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.261][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:14.262][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:14.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.264][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.270][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:14.272][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:14.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.274][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.280][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:10:14.281][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:14.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.284][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.290][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.291][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.293][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.299][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:14.301][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:14.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.303][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.349][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-50943-content.xml".
biodb.DEBUG[2025-03-01 16:10:14.351][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:10:14.353][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-03-01 16:10:14.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:10:14.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:10:14.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:10:14.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:10:14.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:10:14.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:10:14.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:10:14.402][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:14.403][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:14.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.405][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:14.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:14.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.415][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:14.416][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:14.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.418][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.422][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:14.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:14.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.427][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:14.429][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:14.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.431][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.435][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:14.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:14.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.440][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:14.441][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:14.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.443][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.448][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:14.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:14.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.453][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:14.454][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:14.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.456][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.460][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:14.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:14.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.465][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:14.467][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:14.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.469][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.477][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:14.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:14.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.488][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.494][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:14.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:14.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.498][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:14.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:14.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:14.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:14.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.508][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:14.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:14.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:14.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:14.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:14.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:14.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:14.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:14.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:14.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:14.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:14.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:14.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:14.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:14.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:10:14.541][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 50943.
biodb.TRACE[2025-03-01 16:10:14.544][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:14.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:14.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.549][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:14.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:14.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.553][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.558][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:14.563][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:14.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:14.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:10:14.568][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-03-01 16:10:14.569][private$loadEntries] Creating entries from ids [1]: "CCDS14323.1".
biodb.DEBUG[2025-03-01 16:10:14.570][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-01 16:10:14.572][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS14323.1".
biodb.TRACE[2025-03-01 16:10:14.574][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-01 16:10:14.575][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-01 16:10:14.576][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:10:14.577][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-03-01 16:10:14.579][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-01 16:10:14.580][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-01 16:10:14.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:10:14.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:10:14.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:10:14.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:10:14.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:10:14.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:10:14.595][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.DEBUG[2025-03-01 16:10:14.596][scheduler$sendRequest] Getting content of get URL request "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.DEBUG[2025-03-01 16:10:14.599][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:14.601][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:10:14.602][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-03-01 16:10:14.608][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 does not exist.
biodb.TRACE[2025-03-01 16:10:14.609][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:14.610][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:14.611][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-03-01 16:10:14.724][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:10:14.726][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:14.727][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:10:14.729][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-03-01 16:10:14.735][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 does not exist.
biodb.TRACE[2025-03-01 16:10:14.736][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:14.738][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:14.739][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-03-01 16:10:14.743][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:10:14.744][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:14.745][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:10:14.747][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-03-01 16:10:14.752][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 does not exist.
biodb.TRACE[2025-03-01 16:10:14.753][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:14.754][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:14.755][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-03-01 16:10:14.759][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:10:14.760][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:14.761][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:10:14.763][rule$waitAsNeeded] Wait 0.839479 second(s).
biodb.TRACE[2025-03-01 16:10:15.616][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-03-01 16:10:15.623][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 does not exist.
biodb.TRACE[2025-03-01 16:10:15.625][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:15.626][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:15.627][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-03-01 16:10:15.631][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:10:15.632][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:15.633][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:10:15.635][rule$waitAsNeeded] Wait 0.0942271 second(s).
biodb.TRACE[2025-03-01 16:10:15.741][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-03-01 16:10:15.748][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 does not exist.
biodb.TRACE[2025-03-01 16:10:15.750][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:15.751][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:15.752][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-03-01 16:10:15.756][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:10:15.757][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:15.758][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:10:15.760][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-03-01 16:10:15.766][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 does not exist.
biodb.TRACE[2025-03-01 16:10:15.767][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:15.768][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:15.769][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-03-01 16:10:15.883][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:10:15.884][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:15.885][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:10:15.887][rule$waitAsNeeded] Wait 0.728635 second(s).
biodb.TRACE[2025-03-01 16:10:16.633][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-03-01 16:10:16.640][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 does not exist.
biodb.TRACE[2025-03-01 16:10:16.641][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:16.643][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:16.644][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-03-01 16:10:16.648][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:10:16.649][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:16.650][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:10:16.652][rule$waitAsNeeded] Wait 0.0887492 second(s).
biodb.TRACE[2025-03-01 16:10:16.743][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-03-01 16:10:16.750][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 does not exist.
biodb.TRACE[2025-03-01 16:10:16.752][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:16.753][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:16.754][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-03-01 16:10:16.758][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:10:16.759][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:16.760][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:10:16.762][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-03-01 16:10:16.768][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 does not exist.
biodb.TRACE[2025-03-01 16:10:16.769][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:16.770][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:16.771][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-03-01 16:10:16.885][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:10:16.886][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:16.887][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:10:16.889][rule$waitAsNeeded] Wait 0.74398 second(s).
biodb.TRACE[2025-03-01 16:10:17.651][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1".
biodb.TRACE[2025-03-01 16:10:17.657][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1 does not exist.
biodb.TRACE[2025-03-01 16:10:17.658][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:17.660][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:17.661][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14323.1).
biodb.INFO [2025-03-01 16:10:17.665][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:10:17.668][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS14323.1.html"
biodb.DEBUG[2025-03-01 16:10:17.670][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-01 16:10:17.671][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:10:17.673][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-03-01 16:10:17.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:10:17.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:10:17.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:10:17.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:10:17.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:10:17.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:10:17.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:10:17.695][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:17.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:17.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.700][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:17.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:17.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:10:17.733][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-03-01 16:10:17.734][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.TRACE[2025-03-01 16:10:17.735][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:10:17.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:10:17.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.740][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:10:17.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:10:17.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.745][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:10:17.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:10:17.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.750][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:10:17.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:10:17.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.765][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:17.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:17.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.806][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:17.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:17.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.810][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:17.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:17.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.815][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:17.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:17.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.853][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.854][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.856][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:17.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:17.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.872][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:17.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:17.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.877][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:17.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:17.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.882][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:17.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:17.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.886][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:17.888][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:17.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.890][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.891][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:17.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:17.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.905][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:17.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:17.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.910][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:17.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:17.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.915][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:17.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:17.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.920][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:17.921][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:17.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.923][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.924][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:17.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:17.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.938][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:17.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:17.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.943][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:17.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:17.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.948][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:17.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:17.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.953][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:17.954][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:17.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.956][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.957][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:17.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:17.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.972][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:17.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:17.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.977][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:17.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:17.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.981][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:17.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:17.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.986][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:17.987][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:17.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.990][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:17.991][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:17.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:17.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:17.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.005][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:18.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:18.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.010][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:18.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:18.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.015][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:18.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:18.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.019][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:18.021][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:18.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.023][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.024][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:18.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:18.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.038][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:18.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:18.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:10:18.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:18.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:10:18.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:18.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.053][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:18.054][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:18.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.056][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.057][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:18.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:18.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.072][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:10:18.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:18.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.077][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:18.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:18.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.082][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:18.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:18.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.087][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:18.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:18.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.092][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.097][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.102][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:10:18.106][private$computeField] Compute value for field "aa.seq".
biodb.TRACE[2025-03-01 16:10:18.108][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:18.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:18.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.113][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:10:18.114][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:18.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.116][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.117][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:10:18.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:18.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.157][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:18.159][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:18.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.161][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.167][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:18.169][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:18.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.171][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.183][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:18.185][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:18.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.187][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.193][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:18.194][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:18.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.197][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.203][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:10:18.204][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:18.205][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.206][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.212][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.214][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.216][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.222][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:18.224][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:18.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.226][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.253][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-5551-content.xml".
biodb.DEBUG[2025-03-01 16:10:18.255][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:10:18.257][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-03-01 16:10:18.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:10:18.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:10:18.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:10:18.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:10:18.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:10:18.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:10:18.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:10:18.282][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:18.283][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:18.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.286][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:18.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:18.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.293][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:18.294][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:18.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.296][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.299][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:10:18.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:10:18.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.304][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:18.305][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:18.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.307][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.309][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:10:18.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:10:18.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.314][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:18.316][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:18.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.318][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.320][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:10:18.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:10:18.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.325][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:18.326][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:18.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.329][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.331][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:10:18.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:10:18.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.336][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:18.337][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:18.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.340][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.343][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:18.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:10:18.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.349][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.354][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:18.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:18.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.359][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:18.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:18.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:18.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:18.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.369][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:18.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:10:18.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:18.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:18.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:18.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:18.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:18.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:18.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:18.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:18.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:18.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:18.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:10:18.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:10:18.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:10:18.403][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 5551.
biodb.TRACE[2025-03-01 16:10:18.405][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:18.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:18.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.410][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:10:18.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:10:18.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.415][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.420][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:10:18.425][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:10:18.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:10:18.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:10:18.429][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-03-01 16:10:18.431][private$loadEntries] Creating entries from ids [1]: "CCDS7305.1".
biodb.DEBUG[2025-03-01 16:10:18.432][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-01 16:10:18.434][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS7305.1".
biodb.TRACE[2025-03-01 16:10:18.435][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-01 16:10:18.437][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-01 16:10:18.438][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:10:18.439][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-03-01 16:10:18.441][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-01 16:10:18.442][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-01 16:10:18.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:10:18.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:10:18.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:10:18.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:10:18.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:10:18.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:10:18.457][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[2025-03-01 16:10:18.459][scheduler$sendRequest] Getting content of get URL request "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.DEBUG[2025-03-01 16:10:18.462][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:18.463][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:10:18.465][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-03-01 16:10:29.516][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 does not exist.
biodb.TRACE[2025-03-01 16:10:29.517][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:29.519][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:29.520][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-03-01 16:10:40.607][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:10:40.609][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:10:40.610][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:10:40.612][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-03-01 16:10:51.669][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 does not exist.
biodb.TRACE[2025-03-01 16:10:51.670][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:10:51.672][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:10:51.673][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-03-01 16:11:02.825][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:11:02.827][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:11:02.828][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:11:02.830][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-03-01 16:11:13.891][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 does not exist.
biodb.TRACE[2025-03-01 16:11:13.893][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:11:13.894][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:11:13.895][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-03-01 16:11:25.037][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:11:25.039][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:11:25.040][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:11:25.042][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-03-01 16:11:36.089][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 does not exist.
biodb.TRACE[2025-03-01 16:11:36.090][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:11:36.092][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:11:36.093][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-03-01 16:11:47.141][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:11:47.143][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:11:47.144][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:11:47.146][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-03-01 16:11:58.193][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 does not exist.
biodb.TRACE[2025-03-01 16:11:58.195][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:11:58.196][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:11:58.197][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-03-01 16:12:09.245][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:12:09.247][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:12:09.248][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:12:09.250][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-03-01 16:12:20.296][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 does not exist.
biodb.TRACE[2025-03-01 16:12:20.297][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:12:20.299][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:12:20.300][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-03-01 16:12:31.348][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:12:31.350][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:12:31.351][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:12:31.353][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-03-01 16:12:42.399][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 does not exist.
biodb.TRACE[2025-03-01 16:12:42.400][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:12:42.402][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:12:42.403][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-03-01 16:12:53.466][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:12:53.468][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:12:53.469][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:12:53.471][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-03-01 16:13:04.517][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 does not exist.
biodb.TRACE[2025-03-01 16:13:04.518][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:13:04.520][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:13:04.521][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-03-01 16:13:04.768][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:13:04.769][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:13:04.770][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:13:04.772][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-03-01 16:13:04.778][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 does not exist.
biodb.TRACE[2025-03-01 16:13:04.779][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:13:04.780][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:13:04.781][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-03-01 16:13:04.785][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:13:04.787][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:13:04.788][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:13:04.789][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1".
biodb.TRACE[2025-03-01 16:13:04.795][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1 does not exist.
biodb.TRACE[2025-03-01 16:13:04.796][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:13:04.797][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:13:04.799][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1).
biodb.INFO [2025-03-01 16:13:04.802][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS7305.1". Retrying connection to server...
biodb.TRACE[2025-03-01 16:13:04.805][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS7305.1.html"
biodb.DEBUG[2025-03-01 16:13:04.808][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-01 16:13:04.809][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:13:04.811][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-03-01 16:13:04.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:13:04.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:13:04.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:13:04.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:13:04.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:13:04.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:13:04.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:13:04.829][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:04.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:04.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.834][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:04.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:04.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:04.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:04.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:04.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:04.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:04.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:04.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:04.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:04.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:04.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:04.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:04.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:04.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:13:04.869][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-03-01 16:13:04.870][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.TRACE[2025-03-01 16:13:04.872][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:13:04.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:13:04.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.876][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:13:04.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:13:04.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.881][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:13:04.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:13:04.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.886][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:13:04.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:13:04.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:04.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:04.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.903][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:13:04.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:13:04.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:04.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:04.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:04.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:04.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:04.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:04.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:04.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:04.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:04.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:04.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:04.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:04.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.949][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:13:04.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:13:04.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.967][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:13:04.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:13:04.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:04.972][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:13:04.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:13:04.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:04.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:05.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:05.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:05.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:05.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:05.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:05.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.515][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:05.517][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:05.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.520][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:05.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:05.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.536][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:13:05.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:13:05.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.541][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:13:05.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:13:05.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.545][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:13:05.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:13:05.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.550][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:13:05.552][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:13:05.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.554][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.555][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:13:05.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:13:05.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.570][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:13:05.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:13:05.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.575][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:13:05.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:13:05.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.580][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:13:05.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:13:05.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.585][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:13:05.586][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:13:05.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.589][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.590][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:13:05.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:13:05.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.605][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:05.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:05.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.611][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:05.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:05.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.616][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:05.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:05.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.622][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:05.623][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:05.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.626][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.627][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:05.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:05.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.642][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.647][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.652][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.657][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.658][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.661][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.662][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.676][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:13:05.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:13:05.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.681][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:13:05.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:13:05.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.686][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:13:05.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:13:05.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.691][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:13:05.692][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:13:05.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.695][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.696][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:13:05.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:13:05.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.710][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:13:05.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:13:05.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:13:05.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:13:05.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.720][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:13:05.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:13:05.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.724][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:13:05.726][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:13:05.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.728][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.729][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:13:05.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:13:05.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.743][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:13:05.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:13:05.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.748][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:13:05.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:13:05.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.753][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:13:05.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:13:05.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.757][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:13:05.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:13:05.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.762][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.767][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.772][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:13:05.776][private$computeField] Compute value for field "aa.seq".
biodb.TRACE[2025-03-01 16:13:05.777][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:13:05.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:13:05.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.782][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:13:05.783][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:13:05.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.786][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.787][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:13:05.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:13:05.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.827][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:13:05.828][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:13:05.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.831][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.837][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:05.838][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:05.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.841][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.847][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:13:05.848][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:13:05.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.851][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.857][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:13:05.858][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:13:05.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.860][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.866][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:13:05.868][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:13:05.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.870][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.876][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.877][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:05.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.880][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:05.886][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:05.887][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:05.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:05.889][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.270][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-916-content.xml".
biodb.DEBUG[2025-03-01 16:13:07.272][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:13:07.274][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-03-01 16:13:07.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:13:07.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:13:07.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:13:07.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:13:07.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:13:07.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:13:07.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:13:07.299][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:07.300][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:07.301][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.302][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:07.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:07.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.310][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:13:07.311][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:13:07.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.313][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.315][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:13:07.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:13:07.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.320][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:13:07.322][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:13:07.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.324][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.326][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:13:07.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:13:07.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.331][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:13:07.332][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:13:07.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.334][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.336][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:13:07.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:13:07.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.341][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:13:07.343][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:13:07.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.345][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.347][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:13:07.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:13:07.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.352][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:07.359][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:07.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.362][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.365][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:07.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:13:07.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.371][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:07.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:07.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.376][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:13:07.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:13:07.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.381][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:13:07.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:13:07.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:07.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:07.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.390][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:13:07.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:13:07.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:07.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:07.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:07.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:07.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:07.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:07.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:07.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:07.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:07.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:07.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:13:07.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:13:07.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:13:07.424][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 916.
biodb.TRACE[2025-03-01 16:13:07.426][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:13:07.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:13:07.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.431][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:13:07.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:13:07.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.436][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:07.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:07.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.441][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:07.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:07.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:13:07.446][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:07.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:13:07.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:13:07.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:13:07.450][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-03-01 16:13:07.452][private$loadEntries] Creating entries from ids [1]: "CCDS31685.1".
biodb.DEBUG[2025-03-01 16:13:07.453][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-01 16:13:07.455][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS31685.1".
biodb.TRACE[2025-03-01 16:13:07.456][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-01 16:13:07.458][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-01 16:13:07.459][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:13:07.460][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-03-01 16:13:07.462][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-01 16:13:07.463][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-01 16:13:07.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:13:07.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:13:07.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:13:07.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:13:07.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:13:07.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:13:07.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:13:07.479][scheduler$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[2025-03-01 16:13:07.483][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:13:07.484][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:13:07.485][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-03-01 16:13:07.491][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 does not exist.
biodb.TRACE[2025-03-01 16:13:07.493][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:13:07.494][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:13:07.496][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-03-01 16:13:07.500][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:13:07.501][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:13:07.502][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:13:07.504][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-03-01 16:13:07.509][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 does not exist.
biodb.TRACE[2025-03-01 16:13:07.510][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:13:07.512][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:13:07.513][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-03-01 16:13:07.516][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:13:07.517][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:13:07.519][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:13:07.520][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-03-01 16:13:07.526][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 does not exist.
biodb.TRACE[2025-03-01 16:13:07.527][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:13:07.528][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:13:07.529][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-03-01 16:13:07.533][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:13:07.534][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:13:07.535][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:13:07.536][rule$waitAsNeeded] Wait 0.948968 second(s).
biodb.TRACE[2025-03-01 16:13:08.493][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-03-01 16:13:08.500][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 does not exist.
biodb.TRACE[2025-03-01 16:13:08.502][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:13:08.503][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:13:08.504][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-03-01 16:13:08.508][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:13:08.509][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:13:08.510][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:13:08.512][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-03-01 16:13:08.517][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 does not exist.
biodb.TRACE[2025-03-01 16:13:08.518][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:13:08.520][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:13:08.521][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-03-01 16:13:08.634][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:13:08.635][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:13:08.636][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:13:08.638][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-03-01 16:13:08.644][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 does not exist.
biodb.TRACE[2025-03-01 16:13:08.645][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:13:08.646][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:13:08.647][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-03-01 16:13:08.651][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:13:08.652][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:13:08.653][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:13:08.654][rule$waitAsNeeded] Wait 0.838 second(s).
biodb.TRACE[2025-03-01 16:13:09.510][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-03-01 16:13:20.562][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 does not exist.
biodb.TRACE[2025-03-01 16:13:20.563][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:13:20.565][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:13:20.566][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-03-01 16:13:31.614][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:13:31.616][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:13:31.617][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:13:31.619][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-03-01 16:13:40.611][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 does not exist.
biodb.TRACE[2025-03-01 16:13:40.613][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:13:40.615][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:13:40.616][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-03-01 16:13:51.668][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:13:51.669][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:13:51.671][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:13:51.673][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-03-01 16:14:02.718][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 does not exist.
biodb.TRACE[2025-03-01 16:14:02.720][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:14:02.721][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:14:02.723][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-03-01 16:14:13.771][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:14:13.773][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:14:13.775][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:14:13.777][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1".
biodb.TRACE[2025-03-01 16:14:24.821][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1 does not exist.
biodb.TRACE[2025-03-01 16:14:24.823][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:14:24.825][getUrlRequestResult] URL "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:14:24.826][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS31685.1).
biodb.INFO [2025-03-01 16:14:35.874][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:14:35.878][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS31685.1.html"
biodb.DEBUG[2025-03-01 16:14:35.880][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-01 16:14:35.882][self$createEntryFromContent] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:14:35.883][self$createEntryFromContent] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-03-01 16:14:35.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:14:35.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:14:35.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:14:35.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:14:35.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:14:35.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:14:35.898][FUN] Functions in observer BiodbConfig: [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[2025-03-01 16:14:35.900][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:35.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:35.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.905][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:35.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:35.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:35.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:35.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:35.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:35.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:35.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:35.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:35.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:35.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:35.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:35.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:35.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:35.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:14:35.939][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-03-01 16:14:35.940][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.TRACE[2025-03-01 16:14:35.941][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:14:35.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:14:35.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.946][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:14:35.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:14:35.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.951][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:14:35.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:14:35.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.956][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:14:35.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:14:35.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:35.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:35.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.972][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:35.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:35.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:35.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:35.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:35.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:35.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:35.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:35.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:35.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:35.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:35.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:36.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:36.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:36.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:36.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:36.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.013][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:36.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:36.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.018][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:36.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:36.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.023][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:36.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:36.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:36.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:36.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:36.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:36.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:36.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:36.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.755][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:36.757][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:36.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.759][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:36.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:36.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.775][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:14:36.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:36.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.780][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:36.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:36.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.784][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:36.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:36.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.789][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:14:36.791][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:36.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.793][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.794][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:14:36.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:36.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.808][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:14:36.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:14:36.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.813][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:14:36.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:14:36.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.818][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:14:36.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:14:36.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.823][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:14:36.824][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:14:36.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.826][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.828][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:14:36.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:14:36.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.850][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:14:36.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:14:36.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.855][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:14:36.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:14:36.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.860][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:14:36.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:14:36.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.864][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:14:36.866][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:14:36.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.868][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.869][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:14:36.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:14:36.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.883][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:36.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:36.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.888][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:36.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:36.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.893][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:36.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:36.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.898][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:36.899][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:36.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.901][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.903][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:36.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:36.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.918][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:14:36.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:14:36.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.924][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:14:36.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:14:36.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.929][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:14:36.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:14:36.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.934][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:14:36.936][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:14:36.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.938][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.939][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:14:36.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:14:36.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:14:36.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:14:36.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.960][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:14:36.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:14:36.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:14:36.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:14:36.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.970][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:14:36.972][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:14:36.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.974][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.975][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:14:36.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:14:36.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.989][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:14:36.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:14:36.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.994][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:14:36.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:14:36.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:36.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:36.999][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:14:37.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:14:37.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.004][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:14:37.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:14:37.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.009][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:37.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:37.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.014][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:37.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:37.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.019][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:37.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:37.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:14:37.024][private$computeField] Compute value for field "aa.seq".
biodb.TRACE[2025-03-01 16:14:37.025][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:14:37.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:14:37.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.030][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:14:37.031][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:14:37.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.034][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.035][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-03-01 16:14:37.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:14:37.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.075][ef$get] Asked field names are: aa.seq.location.
biodb.TRACE[2025-03-01 16:14:37.077][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:14:37.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.079][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.085][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.087][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.089][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.095][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:14:37.097][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:14:37.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.099][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.105][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:37.106][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:37.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.109][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.115][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:14:37.116][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:14:37.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.119][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.125][ef$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:37.126][ef$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:37.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.128][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.135][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:14:37.136][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:14:37.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.233][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-9606-content.xml".
biodb.DEBUG[2025-03-01 16:14:37.236][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:14:37.237][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-03-01 16:14:37.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:14:37.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:14:37.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:14:37.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:14:37.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:14:37.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:14:37.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:14:37.254][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.255][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.258][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.264][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:14:37.265][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:14:37.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.267][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.269][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:14:37.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:14:37.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.274][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:14:37.275][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:14:37.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.277][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.279][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:14:37.280][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:37.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.282][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.284][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:14:37.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:37.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.288][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:14:37.290][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:14:37.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.292][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.293][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:14:37.294][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:14:37.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.298][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.299][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:37.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:37.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.304][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:37.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:37.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.314][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:37.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:37.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:14:37.348][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 9606.
biodb.TRACE[2025-03-01 16:14:37.351][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:14:37.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:14:37.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.356][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:14:37.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:14:37.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.361][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:37.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:14:37.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.366][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:14:37.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:14:37.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.371][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:14:37.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:14:37.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.376][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:14:37.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:14:37.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.380][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:14:37.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:14:37.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.396][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:37.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:37.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.444][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:37.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:37.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.449][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:37.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:37.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.453][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:37.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:14:37.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.580][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.582][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.584][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.599][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:14:37.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:37.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.604][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:37.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:37.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.609][self$getBiodb()$getEntryFields()$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:37.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:37.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.614][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:14:37.615][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:37.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.618][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.619][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:14:37.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:37.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.633][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:14:37.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:14:37.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.638][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:14:37.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:14:37.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.643][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:14:37.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:14:37.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.648][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:14:37.649][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:14:37.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.651][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.652][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:14:37.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:14:37.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.667][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:14:37.668][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:14:37.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.670][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.677][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:14:37.678][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:14:37.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.680][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:14:37.686][ef$get] Asked field names are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:37.688][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:14:37.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:14:37.690][ef$get] fields variable is a list.
biodb.INFO [2025-03-01 16:14:37.701][biodb::testThat]
biodb.INFO [2025-03-01 16:14:37.702][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-01 16:14:37.704][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:14:37.705][biodb::testThat]
biodb.DEBUG[2025-03-01 16:14:37.708][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2025-03-01 16:14:37.709][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
biodb.TRACE[2025-03-01 16:14:37.711][cch$loadFileContent] Trying to load 8 files from cache: [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.TRACE[2025-03-01 16:14:37.714][cch$loadFileContent] file.exist = [8]: "FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE".
biodb.TRACE[2025-03-01 16:14:51.853][loadFileContents] Loaded 7 files from cache: [7]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/3002.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/3627.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/4316.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/50943.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/5551.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/916.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/9606.xml".
biodb.DEBUG[2025-03-01 16:14:51.856][conn$getEntryContent] 7 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:14:51.857][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-03-01 16:14:51.858][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-01 16:14:51.859][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-03-01 16:14:51.861][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-01 16:14:51.868][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[2025-03-01 16:14:51.871][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:14:51.872][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:14:51.873][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-03-01 16:15:02.922][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml does not exist.
biodb.TRACE[2025-03-01 16:15:02.924][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:15:02.925][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:15:02.927][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-03-01 16:15:14.005][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:15:14.007][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:15:14.009][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:15:14.010][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-03-01 16:15:25.056][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml does not exist.
biodb.TRACE[2025-03-01 16:15:25.058][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:15:25.060][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:15:25.061][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-03-01 16:15:36.108][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:15:36.110][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:15:36.112][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:15:36.114][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-03-01 16:15:47.159][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml does not exist.
biodb.TRACE[2025-03-01 16:15:47.161][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:15:47.162][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:15:47.164][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-03-01 16:15:58.213][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:15:58.214][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:15:58.215][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:15:58.217][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-03-01 16:16:09.263][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml does not exist.
biodb.TRACE[2025-03-01 16:16:09.265][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:16:09.266][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:16:09.268][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-03-01 16:16:20.316][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:16:20.317][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:16:20.318][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:16:20.320][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-03-01 16:16:31.367][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml does not exist.
biodb.TRACE[2025-03-01 16:16:31.369][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:16:31.371][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:16:31.373][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-03-01 16:16:42.419][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:16:42.420][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:16:42.422][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:16:42.423][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-03-01 16:16:53.469][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml does not exist.
biodb.TRACE[2025-03-01 16:16:53.471][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:16:53.472][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:16:53.474][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-03-01 16:17:04.522][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:17:04.524][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:17:04.525][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:17:04.527][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-03-01 16:17:15.572][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml does not exist.
biodb.TRACE[2025-03-01 16:17:15.574][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:17:15.575][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:17:15.577][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-03-01 16:17:26.624][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:17:26.626][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:17:26.627][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:17:26.629][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-03-01 16:17:37.676][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml does not exist.
biodb.TRACE[2025-03-01 16:17:37.677][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:17:37.678][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:17:37.680][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-03-01 16:17:48.745][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:17:48.747][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:17:48.748][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:17:48.750][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-03-01 16:17:59.796][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml does not exist.
biodb.TRACE[2025-03-01 16:17:59.798][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:17:59.799][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:17:59.801][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-03-01 16:18:10.849][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:18:10.850][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:18:10.852][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:18:10.854][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml".
biodb.TRACE[2025-03-01 16:18:21.899][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml does not exist.
biodb.TRACE[2025-03-01 16:18:21.901][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:18:21.902][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:18:21.903][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833&retmode=xml).
biodb.INFO [2025-03-01 16:18:32.952][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:18:32.954][private$checkXml] XML contains error messages. At least one of the IDs to retrieve is wrong.
biodb.TRACE[2025-03-01 16:18:32.959][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/2833.xml"
biodb.DEBUG[2025-03-01 16:18:32.964][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-01 16:18:32.966][self$createEntryFromContent] Creating NCBI Gene entries from 8 content(s).
biodb.DEBUG[2025-03-01 16:18:32.968][self$createEntryFromContent] Parsing 8 NCBI Gene entries.
biodb.DEBUG[2025-03-01 16:18:32.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:18:32.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:18:32.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:18:32.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:18:32.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:18:32.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:18:32.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:18:32.988][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:32.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:32.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:32.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:32.994][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:32.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:32.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:32.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:18:33.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:18:33.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:18:33.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:18:33.015][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:18:33.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:18:33.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:18:33.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:18:33.035][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.037][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.040][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.049][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:18:33.050][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:18:33.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.053][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.055][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:18:33.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:18:33.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.061][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:18:33.063][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:18:33.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.065][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.068][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:18:33.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:18:33.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.074][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:18:33.075][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:18:33.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.078][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.080][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:18:33.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:18:33.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.086][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:18:33.088][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:18:33.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.090][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.093][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:18:33.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:18:33.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.099][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.100][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.103][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.107][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.117][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:18:33.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:18:33.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.123][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.128][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.140][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:18:33.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:18:33.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:18:33.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:18:33.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:18:33.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:18:33.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:18:33.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:18:33.200][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.202][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.219][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.230][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:18:33.231][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:18:33.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.234][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.237][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:18:33.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:18:33.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.243][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:18:33.244][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:18:33.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.247][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.250][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:18:33.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:18:33.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.256][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:18:33.258][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:18:33.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.261][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.265][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:18:33.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:18:33.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.271][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:18:33.272][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:18:33.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.275][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.279][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:18:33.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:18:33.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.284][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.286][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.289][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.295][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.305][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:18:33.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:18:33.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.311][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.317][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.328][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:18:33.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:18:33.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:18:33.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:18:33.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:18:33.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:18:33.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:18:33.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:18:33.378][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.379][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.382][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.390][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:18:33.392][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:18:33.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.394][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.397][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:18:33.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:18:33.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.403][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:18:33.405][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:18:33.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.407][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.410][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:18:33.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:18:33.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.416][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:18:33.417][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:18:33.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.420][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.423][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:18:33.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:18:33.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.429][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:18:33.430][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:18:33.431][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.433][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.436][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:18:33.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:18:33.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.441][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.442][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.444][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.449][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.456][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:18:33.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:18:33.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.461][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.466][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.476][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:18:33.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:18:33.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:18:33.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:18:33.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:18:33.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:18:33.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:18:33.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:18:33.543][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.544][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.547][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.556][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:18:33.557][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:18:33.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.560][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.564][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:18:33.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:18:33.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.569][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:18:33.570][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:18:33.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.573][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.577][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:18:33.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:18:33.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.582][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:18:33.583][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:18:33.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.585][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.590][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:18:33.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:18:33.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.595][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:18:33.596][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:18:33.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.598][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.603][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:18:33.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:18:33.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.607][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.609][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.611][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.620][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.632][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:18:33.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:18:33.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.637][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.642][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.651][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:18:33.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:18:33.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:18:33.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:18:33.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:18:33.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:18:33.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:18:33.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:18:33.693][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.695][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.697][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.704][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:18:33.705][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:18:33.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.707][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.709][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:18:33.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:18:33.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.714][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:18:33.715][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:18:33.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.718][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.720][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:18:33.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:18:33.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.725][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:18:33.726][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:18:33.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.728][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.730][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:18:33.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:18:33.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.735][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:18:33.736][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:18:33.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.738][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.741][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:18:33.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:18:33.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.745][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.747][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.749][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.752][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.759][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:18:33.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:18:33.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.763][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.768][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.778][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:18:33.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:18:33.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:18:33.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:18:33.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:18:33.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:18:33.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:18:33.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:18:33.820][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.821][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.824][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.831][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:18:33.832][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:18:33.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.834][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.836][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:18:33.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:18:33.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.841][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:18:33.842][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:18:33.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.845][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.847][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:18:33.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:18:33.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.858][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:18:33.859][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:18:33.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.861][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.863][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:18:33.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:18:33.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.868][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:18:33.869][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:18:33.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.872][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.874][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:18:33.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:18:33.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.879][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.880][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.882][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.885][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.892][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:18:33.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:18:33.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.897][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.901][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.911][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:18:33.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:18:33.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:18:33.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:18:33.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:18:33.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:18:33.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:18:33.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:18:33.944][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.946][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.948][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:33.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.954][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:18:33.955][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:18:33.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.958][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.959][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-01 16:18:33.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-01 16:18:33.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.964][ef$get] Asked field names are: location.
biodb.TRACE[2025-03-01 16:18:33.965][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-03-01 16:18:33.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.967][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.969][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:18:33.970][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:18:33.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.972][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.974][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-03-01 16:18:33.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-03-01 16:18:33.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.979][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-03-01 16:18:33.980][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:18:33.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.982][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.983][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.985][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-03-01 16:18:33.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.987][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.988][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.993][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:33.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:33.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:33.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:33.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.002][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:34.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-03-01 16:18:34.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:18:34.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:18:34.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:18:34.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:18:34.143][self$createEntryFromContent] Accession numbers: NA, 3002, 3627, 4316, 50943, 5551, 916, 9606.
biodb.DEBUG[2025-03-01 16:18:34.145][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-01 16:18:34.162][biodb::testThat]
biodb.INFO [2025-03-01 16:18:34.164][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-01 16:18:34.165][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:18:34.166][biodb::testThat]
biodb.TRACE[2025-03-01 16:18:34.169][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:18:34.171][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:18:34.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:18:34.173][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:18:34.175][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.INFO [2025-03-01 16:18:34.232][biodb::testThat]
biodb.INFO [2025-03-01 16:18:34.234][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-01 16:18:34.235][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:18:34.236][biodb::testThat]
biodb.INFO [2025-03-01 16:18:34.282][biodb::testThat]
biodb.INFO [2025-03-01 16:18:34.283][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-01 16:18:34.284][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:18:34.286][biodb::testThat]
biodb.INFO [2025-03-01 16:18:34.335][biodb::testThat]
biodb.INFO [2025-03-01 16:18:34.336][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-01 16:18:34.338][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:18:34.339][biodb::testThat]
biodb.INFO [2025-03-01 16:18:34.353][biodb::testThat]
biodb.INFO [2025-03-01 16:18:34.354][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-01 16:18:34.355][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:18:34.356][biodb::testThat]
biodb.INFO [2025-03-01 16:18:34.367][biodb::testThat]
biodb.INFO [2025-03-01 16:18:34.368][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-01 16:18:34.369][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:18:34.370][biodb::testThat]
biodb.DEBUG[2025-03-01 16:18:34.375][function(conn, opt)] Trying to download "https://www.ncbi.nlm.nih.gov/gene?term=2833".
biodb.DEBUG[2025-03-01 16:18:45.426][getUrlContent] Use base::url() for downloading content of URL https://www.ncbi.nlm.nih.gov/gene?term=2833.
biodb.INFO [2025-03-01 16:18:56.557][biodb::testThat]
biodb.INFO [2025-03-01 16:18:56.558][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-01 16:18:56.560][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:18:56.561][biodb::testThat]
biodb.INFO [2025-03-01 16:18:56.569][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-01 16:18:56.571][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.gene from the request scheduler
biodb.INFO [2025-03-01 16:18:56.572][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.DEBUG[2025-03-01 16:18:56.574][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.ccds from the request scheduler
biodb.INFO [2025-03-01 16:18:56.581][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-03-01 16:18:56.582][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-01 16:18:56.583][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:18:56.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:18:56.585][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:18:56.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:18:56.587][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:18:56.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-01 16:19:01.582][biodb::testContext]
biodb.INFO [2025-03-01 16:19:01.584][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:19:01.586][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2025-03-01 16:19:01.587][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:19:01.588][biodb::testContext]
biodb.INFO [2025-03-01 16:19:01.591][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:19:01.594][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-01 16:19:01.599][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:19:01.601][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-01 16:19:01.602][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-01 16:19:01.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.607][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-01 16:19:01.608][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-01 16:19:01.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.612][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-01 16:19:01.614][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-01 16:19:01.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.618][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-01 16:19:01.619][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-01 16:19:01.621][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-01 16:19:01.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.624][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[2025-03-01 16:19:01.625][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-01 16:19:01.626][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-01 16:19:01.628][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-01 16:19:01.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.632][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-01 16:19:01.633][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-01 16:19:01.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.637][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[2025-03-01 16:19:01.638][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-01 16:19:01.639][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-01 16:19:01.641][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-01 16:19:01.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.645][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-01 16:19:01.646][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-01 16:19:01.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.650][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[2025-03-01 16:19:01.651][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-01 16:19:01.652][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-01 16:19:01.653][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-01 16:19:01.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.658][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:19:01.659][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-01 16:19:01.660][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-01 16:19:01.662][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-01 16:19:01.663][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-01 16:19:01.664][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-01 16:19:01.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.669][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-01 16:19:01.670][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-01 16:19:01.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.675][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-01 16:19:01.676][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-01 16:19:01.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.680][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-01 16:19:01.682][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-01 16:19:01.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.686][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-01 16:19:01.688][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-01 16:19:01.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.692][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-01 16:19:01.693][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-01 16:19:01.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.698][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:19:01.699][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-01 16:19:01.703][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-01 16:19:01.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.707][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-01 16:19:01.709][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-01 16:19:01.710][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-01 16:19:01.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.715][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-01 16:19:01.717][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:01.718][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-01 16:19:01.719][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.721][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:19:01.722][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.723][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:19:01.724][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:01.725][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:19:01.727][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:19:01.728][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:19:01.729][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.730][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-01 16:19:01.732][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:19:01.733][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:01.734][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.735][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:19:01.735][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:19:01.735][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:19:01.735][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:19:01.735][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:19:01.737][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:19:01.738][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:01.739][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:01.740][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:19:01.741][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:01.742][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:01.743][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:19:01.745][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:01.746][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:19:01.747][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:19:01.748][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:01.749][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:01.751][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-01 16:19:01.753][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:01.754][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:19:01.755][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.756][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:19:01.757][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.759][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:19:01.760][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:01.761][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:19:01.762][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:19:01.763][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:19:01.765][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.766][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-01 16:19:01.767][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:19:01.768][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:01.769][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.771][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:19:01.771][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:19:01.771][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:19:01.771][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:19:01.771][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:19:01.772][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:19:01.773][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:01.774][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:01.775][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:19:01.776][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:01.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:01.779][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:19:01.780][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:01.781][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:19:01.782][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:19:01.783][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:01.785][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:01.786][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-01 16:19:01.788][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.789][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-01 16:19:01.790][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.791][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:19:01.793][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.794][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:19:01.795][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:01.796][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:19:01.797][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:19:01.799][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:19:01.800][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:01.801][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-01 16:19:01.802][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:19:01.804][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:01.805][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.806][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:01.807][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:19:01.808][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:01.809][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:01.811][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:19:01.812][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:01.813][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:01.814][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:19:01.815][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:01.816][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:19:01.818][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:19:01.819][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:01.820][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:01.821][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-01 16:19:01.823][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.825][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:19:01.826][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.827][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:19:01.828][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.829][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:19:01.831][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:01.832][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:19:01.833][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:19:01.834][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:19:01.835][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:01.837][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-01 16:19:01.838][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:19:01.839][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:01.840][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:01.842][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:01.843][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:19:01.844][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:01.845][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:01.846][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:19:01.847][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:01.848][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:01.850][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:19:01.851][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:01.852][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:19:01.853][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:19:01.854][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:01.855][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:01.857][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:19:01.858][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.915][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[2025-03-01 16:19:01.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.948][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[2025-03-01 16:19:01.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:01.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:01.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:01.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:01.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:01.960][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-01 16:19:01.962][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-01 16:19:01.963][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-01 16:19:01.965][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-01 16:19:01.966][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-01 16:19:01.968][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-01 16:19:01.970][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-01 16:19:01.971][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-01 16:19:01.973][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-01 16:19:01.974][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-01 16:19:01.976][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-01 16:19:01.977][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-01 16:19:01.979][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-01 16:19:01.980][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-01 16:19:01.982][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:19:01.984][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:19:01.985][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-01 16:19:01.987][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-01 16:19:01.988][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-01 16:19:01.990][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-01 16:19:01.991][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-01 16:19:01.993][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-01 16:19:01.995][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-01 16:19:01.996][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-01 16:19:01.998][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-01 16:19:01.999][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-01 16:19:02.001][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-01 16:19:02.002][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-01 16:19:02.004][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-01 16:19:02.006][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-01 16:19:02.007][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-01 16:19:02.009][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-01 16:19:02.010][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-01 16:19:02.012][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-01 16:19:02.014][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-01 16:19:02.015][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-01 16:19:02.017][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-01 16:19:02.018][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-01 16:19:02.020][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-01 16:19:02.021][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-01 16:19:02.023][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-01 16:19:02.024][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-01 16:19:02.026][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-01 16:19:02.028][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-01 16:19:02.029][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-01 16:19:02.031][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:19:02.032][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-01 16:19:02.034][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-01 16:19:02.036][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-01 16:19:02.037][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-01 16:19:02.039][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-01 16:19:02.040][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-01 16:19:02.042][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-01 16:19:02.043][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-01 16:19:02.045][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-01 16:19:02.046][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-01 16:19:02.048][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-01 16:19:02.050][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-01 16:19:02.051][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-01 16:19:02.053][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-01 16:19:02.054][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-01 16:19:02.056][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-01 16:19:02.057][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-01 16:19:02.059][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-01 16:19:02.060][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-01 16:19:02.062][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-01 16:19:02.064][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-01 16:19:02.065][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-01 16:19:02.067][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-01 16:19:02.068][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-01 16:19:02.070][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-01 16:19:02.071][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-01 16:19:02.073][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-01 16:19:02.075][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-01 16:19:02.076][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-01 16:19:02.078][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-01 16:19:02.079][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-01 16:19:02.081][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-01 16:19:02.082][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-01 16:19:02.084][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-01 16:19:02.085][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-01 16:19:02.087][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-01 16:19:02.089][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-01 16:19:02.090][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-01 16:19:02.093][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:19:02.094][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:19:02.095][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.097][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.168][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[2025-03-01 16:19:02.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:19:02.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:19:02.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:02.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:02.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:02.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:02.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:02.229][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[2025-03-01 16:19:02.232][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-03-01 16:19:02.235][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-03-01 16:19:02.237][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.238][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-03-01 16:19:02.239][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.240][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:19:02.242][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.243][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:19:02.244][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.245][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:19:02.246][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-03-01 16:19:02.247][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:19:02.249][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.250][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-03-01 16:19:02.251][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:19:02.252][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-03-01 16:19:02.252][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-03-01 16:19:02.253][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:02.255][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:02.256][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:19:02.257][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:02.258][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:02.261][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:19:02.262][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:02.263][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:02.264][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:19:02.265][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-03-01 16:19:02.265][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-03-01 16:19:02.266][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:19:02.267][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:19:02.269][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.270][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:02.271][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-03-01 16:19:02.273][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.274][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-03-01 16:19:02.275][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.277][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:19:02.278][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.279][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:19:02.280][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.281][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:19:02.282][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-01 16:19:02.284][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:19:02.286][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.287][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-03-01 16:19:02.289][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:19:02.290][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-03-01 16:19:02.290][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-03-01 16:19:02.290][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-03-01 16:19:02.290][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-03-01 16:19:02.290][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-03-01 16:19:02.290][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-03-01 16:19:02.292][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:02.293][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:19:02.294][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:19:02.295][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:02.296][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:02.297][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:19:02.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:02.300][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:02.301][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:19:02.302][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-03-01 16:19:02.302][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-03-01 16:19:02.303][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:19:02.304][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:19:02.306][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.307][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:02.309][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-03-01 16:19:02.311][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:02.312][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-03-01 16:19:02.313][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.314][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:19:02.315][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.317][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:19:02.318][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.319][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:19:02.320][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-01 16:19:02.321][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:19:02.323][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.324][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-03-01 16:19:02.325][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:19:02.326][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-03-01 16:19:02.326][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:19:02.326][self$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[2025-03-01 16:19:02.326][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:19:02.326][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:19:02.326][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:19:02.326][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:19:02.326][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:19:02.326][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:19:02.326][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:19:02.326][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-03-01 16:19:02.326][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:19:02.326][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:19:02.326][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:19:02.328][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:02.329][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:19:02.329][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:19:02.329][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:19:02.330][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-03-01 16:19:02.331][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:02.332][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:02.333][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:19:02.335][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:02.336][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:02.337][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:19:02.338][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-03-01 16:19:02.338][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-03-01 16:19:02.338][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-03-01 16:19:02.339][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:19:02.340][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:19:02.341][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.343][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-03-01 16:19:02.344][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-03-01 16:19:02.346][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.347][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-03-01 16:19:02.349][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.350][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:19:02.351][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.352][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:19:02.353][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.354][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:19:02.356][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-01 16:19:02.357][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:19:02.358][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.359][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-03-01 16:19:02.360][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:19:02.362][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-03-01 16:19:02.362][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-03-01 16:19:02.370][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:19:02.371][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:19:02.372][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-03-01 16:19:02.373][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:02.375][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:02.376][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:19:02.377][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:19:02.378][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:19:02.379][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:19:02.380][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-03-01 16:19:02.380][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-03-01 16:19:02.380][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-03-01 16:19:02.381][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:19:02.382][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:19:02.383][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:19:02.385][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-03-01 16:19:02.386][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-03-01 16:19:02.388][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:19:02.389][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:19:02.391][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-03-01 16:19:02.393][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:19:02.394][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-03-01 16:19:02.402][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2025-03-01 16:19:02.403][super$initialize] Register connector ncbi.pubchem.comp with the request scheduler
biodb.DEBUG[2025-03-01 16:19:02.405][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.pubchem.comp.
biodb.DEBUG[2025-03-01 16:19:02.407][private$addConnectorRules] Create new rule for URL "pubchem.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.comp".
biodb.DEBUG[2025-03-01 16:19:02.408][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-03-01 16:19:02.409][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-03-01 16:19:02.411][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.comp".
biodb.DEBUG[2025-03-01 16:19:02.412][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-03-01 16:19:02.414][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-03-01 16:19:02.415][rule$addConnector] Connector "ncbi.pubchem.comp" is already listed in rule "pubchem.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-03-01 16:19:02.421][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2025-03-01 16:19:02.427][biodb::testThat]
biodb.INFO [2025-03-01 16:19:02.428][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-01 16:19:02.429][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:19:02.430][biodb::testThat]
biodb.TRACE[2025-03-01 16:19:05.471][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2025-03-01 16:19:05.473][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:19:05.477][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-03-01 16:19:05.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:19:05.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:05.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:05.488][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:05.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:05.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:05.491][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.TRACE[2025-03-01 16:19:05.496][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.497][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.499][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.506][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:05.507][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:05.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.509][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.511][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:05.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:05.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.516][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:05.517][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:05.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.519][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.521][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:05.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:05.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.526][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:05.527][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:05.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.529][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.531][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:05.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:05.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.536][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:05.537][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:05.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.539][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.541][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:05.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:05.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.545][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:05.547][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:05.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.549][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.551][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:05.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:05.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.555][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:19:05.557][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:05.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.559][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.560][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:19:05.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:05.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.565][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:05.566][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:05.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.569][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.570][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:05.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:05.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.575][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:05.576][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:05.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.578][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:05.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:05.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.585][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:05.586][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:05.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.588][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:05.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:05.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.595][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:05.596][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:05.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.598][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.600][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:05.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:05.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.604][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:19:05.606][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:05.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.608][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:19:05.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:05.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.614][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:05.615][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:05.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.618][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.619][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:05.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:05.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.624][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:05.625][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:05.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.627][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.629][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:05.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:05.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.634][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-03-01 16:19:05.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:05.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.638][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:05.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:05.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.643][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:05.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:05.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.648][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-03-01 16:19:05.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:05.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.653][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:05.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:05.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.657][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:05.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:05.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.662][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-03-01 16:19:05.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:05.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.667][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:05.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:05.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.671][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:05.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:05.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.676][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-03-01 16:19:05.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:05.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.681][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:05.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:05.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.685][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:05.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:05.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.690][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-03-01 16:19:05.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:05.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.695][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:05.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:05.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.699][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:05.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:05.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:05.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:05.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.709][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:05.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:05.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.713][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:05.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:05.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.723][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:05.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:05.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:19:05.756][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2025-03-01 16:19:05.758][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:19:05.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:19:05.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.763][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:19:05.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:19:05.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.768][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:19:05.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:19:05.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.772][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:19:05.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:19:05.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.777][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:19:05.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:19:05.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.782][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:19:05.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:19:05.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.786][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:19:05.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:19:05.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.803][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:05.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:05.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:05.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:05.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.844][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:05.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:05.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.848][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:05.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:05.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:05.853][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:05.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:05.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:05.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:08.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:08.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:08.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:08.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:08.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:08.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.226][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:08.227][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:08.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.229][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:08.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:08.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.244][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:19:08.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:08.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:08.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:08.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:08.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:08.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.259][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:19:08.260][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:08.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.263][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.264][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:19:08.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:08.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:19:08.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:08.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:08.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:08.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:08.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:08.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.293][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:19:08.294][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:08.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.297][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.298][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:19:08.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:08.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.312][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:08.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:08.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.317][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:08.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:08.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.321][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:08.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:08.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.326][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:08.327][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:08.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.330][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.331][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:08.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:08.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.345][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:08.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:08.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.350][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:08.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:08.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.354][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:08.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:08.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.359][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:08.360][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:08.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.363][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.364][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:08.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:08.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.378][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:08.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:08.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.383][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:08.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:08.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.388][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:08.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:08.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.392][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:08.394][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:08.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.396][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.397][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:08.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:08.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.411][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:08.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:08.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.416][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:08.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:08.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.421][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:08.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:08.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.426][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:08.427][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:08.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.429][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.430][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:08.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:08.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.444][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:08.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:08.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.449][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:08.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:08.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.454][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:08.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:08.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.459][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:08.460][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:08.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.463][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.464][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:08.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:08.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.478][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:08.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:08.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.483][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:08.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:08.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.487][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:08.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:08.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.492][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:08.493][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:08.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.496][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.497][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:08.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:08.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.511][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:08.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:08.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.516][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:08.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:08.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.520][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:08.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:08.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.525][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:08.526][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:08.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.529][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.530][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:08.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:08.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.544][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:08.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:08.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.549][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:08.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:08.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.554][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:08.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:08.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.559][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:08.560][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:08.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.562][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.563][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:08.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:08.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.577][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:08.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:08.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.582][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:08.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:08.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.587][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:08.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:08.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.592][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:08.593][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:08.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.595][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.596][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:08.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:08.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:08.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:08.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.615][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:08.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:08.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:08.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:08.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.625][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:08.626][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:08.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.628][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:08.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:08.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.644][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:08.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:08.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:08.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:08.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.653][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:08.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:08.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.658][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:08.659][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:08.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.661][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:08.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:08.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.677][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:08.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:08.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.688][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:08.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:08.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.693][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:08.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:08.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.697][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:08.699][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:08.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.701][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.702][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:08.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:08.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.716][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:08.717][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:08.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.720][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.726][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:08.727][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:08.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.730][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.736][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:08.737][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:08.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.739][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.746][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:08.747][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:08.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.749][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.756][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:08.757][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:08.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.759][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.766][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:08.767][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:08.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.769][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.776][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:08.777][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:08.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.779][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.786][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:08.787][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:08.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.789][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.796][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:08.797][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:08.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.799][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.805][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:08.807][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:08.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.809][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.815][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:08.816][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:08.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.819][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.825][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:08.826][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:08.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.829][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.835][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:08.836][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:08.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.838][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.845][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:08.846][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:08.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.848][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:08.855][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:08.856][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:08.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:08.858][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.480][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2025-03-01 16:19:09.483][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:19:09.484][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-03-01 16:19:09.486][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:19:09.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:09.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:09.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:09.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:09.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:09.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:19:09.501][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.503][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.505][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.511][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:09.513][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:09.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.515][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.516][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:09.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:09.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.521][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:09.523][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:09.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.525][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.526][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:09.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:09.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.531][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:09.533][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:09.534][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.535][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.536][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:09.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:09.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.541][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:09.542][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:09.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.545][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.546][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:09.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:09.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.551][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:09.552][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:09.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.555][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.556][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:09.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:09.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.561][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:19:09.562][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:09.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.564][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.566][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:19:09.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:09.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.571][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:09.572][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:09.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.574][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.576][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:09.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:09.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.581][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:09.582][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:09.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.584][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:09.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:09.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.590][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:09.592][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:09.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.594][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:09.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:09.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.600][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:09.601][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:09.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.604][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.605][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:09.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:09.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.610][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:19:09.611][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:09.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.613][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:19:09.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:09.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.620][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:09.621][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:09.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.623][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.625][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:09.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:09.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.630][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:09.631][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:09.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.633][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.635][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:09.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:09.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.640][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-03-01 16:19:09.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:09.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.644][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:09.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:09.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.649][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:09.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:09.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.654][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-03-01 16:19:09.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:09.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.658][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:09.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:09.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.663][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:09.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:09.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.668][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-03-01 16:19:09.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:09.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.673][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:09.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:09.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.677][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:09.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:09.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.682][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-03-01 16:19:09.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:09.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.687][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:09.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:09.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.691][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:09.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:09.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.696][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-03-01 16:19:09.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:09.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.701][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:09.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:09.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.705][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:09.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:09.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.710][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:09.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:09.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.715][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:09.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:09.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.720][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:09.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:09.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.729][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:09.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:09.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:19:09.763][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2025-03-01 16:19:09.765][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:19:09.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:19:09.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.770][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:19:09.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:19:09.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.775][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:19:09.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:19:09.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.785][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:19:09.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:19:09.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.790][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:19:09.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:19:09.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.795][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:19:09.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:19:09.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.799][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:19:09.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:19:09.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.816][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:09.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:09.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:09.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:09.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.856][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:09.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:09.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.861][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:09.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:09.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:09.865][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:09.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:09.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:09.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:10.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:10.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:10.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:10.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:10.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:10.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.699][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:10.700][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:10.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.702][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:10.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:10.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:10.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:10.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:10.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:10.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:10.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:10.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.732][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:10.734][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:10.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.736][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:10.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:10.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.751][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:10.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:10.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:10.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:10.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:10.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:10.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.766][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:10.767][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:10.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.769][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:10.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:10.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.785][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:10.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:10.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.790][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:10.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:10.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.794][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:10.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:10.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.799][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:10.800][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:10.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.803][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.804][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:10.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:10.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.818][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:10.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:10.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.823][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:10.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:10.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.828][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:10.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:10.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.832][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:10.834][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:10.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.836][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.837][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:10.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:10.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.851][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:10.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:10.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.856][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:10.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:10.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.861][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:10.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:10.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.866][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:10.867][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:10.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.869][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.871][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:10.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:10.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.885][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:10.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:10.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.890][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:10.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:10.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.895][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:10.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:10.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.899][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:10.901][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:10.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.903][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.904][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:10.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:10.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.918][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:10.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:10.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.924][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:10.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:10.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.928][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:10.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:10.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.933][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:10.934][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:10.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.937][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.938][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:10.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:10.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.952][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:10.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:10.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:10.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:10.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.962][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:10.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:10.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.966][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:10.968][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:10.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.970][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.971][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:10.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:10.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.985][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:10.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:10.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.990][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:10.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:10.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:10.995][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:10.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:10.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:10.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.000][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.001][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.003][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.005][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.019][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.024][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.028][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.033][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.034][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.037][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.038][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.052][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.064][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.069][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.074][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.075][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.077][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.078][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.092][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.097][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.102][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.107][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.108][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.111][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.112][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.126][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.131][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.135][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.140][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.141][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.144][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.145][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:11.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:11.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:11.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:11.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.169][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:11.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:11.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.173][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:11.175][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:11.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.177][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.178][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:11.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:11.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.192][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:11.194][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:11.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.196][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.202][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.204][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.205][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.206][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.212][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.213][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.216][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.222][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.223][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.225][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.232][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.233][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.235][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.242][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.243][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.245][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.252][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:11.253][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:11.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.255][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.262][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:11.263][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:11.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.265][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.272][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:11.273][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:11.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.275][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.281][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:11.283][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:11.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.285][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.292][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:11.294][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:11.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.296][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.302][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:11.303][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:11.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.306][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.312][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:11.313][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:11.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.315][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.322][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:11.323][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:11.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.325][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.331][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:11.333][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:11.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.335][ef$get] fields variable is a list.
biodb.INFO [2025-03-01 16:19:11.346][biodb::testThat]
biodb.INFO [2025-03-01 16:19:11.347][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-01 16:19:11.348][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:19:11.349][biodb::testThat]
biodb.DEBUG[2025-03-01 16:19:11.352][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-03-01 16:19:11.354][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
biodb.TRACE[2025-03-01 16:19:11.358][cch$loadFileContent] Trying to load 2 files from cache: [2]: "2, 65124".
biodb.TRACE[2025-03-01 16:19:11.360][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-03-01 16:19:11.613][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[2025-03-01 16:19:11.615][conn$getEntryContent] 2 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:19:11.616][self$createEntryFromContent] Creating PubChem Compound entries from 2 content(s).
biodb.DEBUG[2025-03-01 16:19:11.618][self$createEntryFromContent] Parsing 2 PubChem Compound entries.
biodb.DEBUG[2025-03-01 16:19:11.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:19:11.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:11.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:11.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:11.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:11.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:11.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:19:11.635][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:11.636][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:11.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.638][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:11.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:11.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.645][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.646][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.648][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.650][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.655][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.656][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.658][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.660][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.665][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.666][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.669][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.670][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.675][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.676][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.679][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.680][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.685][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.686][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.689][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.690][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.695][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:19:11.696][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:11.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.699][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.700][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:19:11.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:11.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.705][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:11.706][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:11.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.709][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.710][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:11.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:11.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.715][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:11.716][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:11.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.719][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.720][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:11.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:11.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.725][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:11.727][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:11.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.729][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:11.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:11.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.735][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:11.737][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:11.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.739][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.741][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:11.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:11.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.746][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:19:11.747][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:11.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.749][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.751][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:19:11.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:11.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.756][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:11.757][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:11.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.759][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.761][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:11.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:11.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.766][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:11.767][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:11.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.769][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.771][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:11.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:11.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.776][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-03-01 16:19:11.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.781][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.785][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.790][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-03-01 16:19:11.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.801][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.806][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.811][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-03-01 16:19:11.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.816][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.821][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.825][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-03-01 16:19:11.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.830][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.835][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.840][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-03-01 16:19:11.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.845][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.849][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.854][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:11.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:11.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.859][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:11.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:11.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.864][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:11.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:11.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:11.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:11.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.873][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:11.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:11.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:11.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:11.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:11.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:11.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:11.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:11.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:19:11.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:19:11.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:19:11.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:19:11.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:19:11.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:19:11.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:19:11.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:19:11.908][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:11.909][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:11.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.912][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:11.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:11.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.918][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.919][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.922][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.924][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:11.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.929][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.930][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.932][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.934][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:11.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.939][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.940][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.942][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.944][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:11.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.949][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.950][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.952][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.954][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:11.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.959][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.960][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.962][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.964][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:11.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.969][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:19:11.970][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:11.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.972][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.974][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:19:11.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:11.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.979][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:11.980][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:11.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.982][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.984][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:19:11.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:19:11.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.989][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:11.990][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:11.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.992][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.994][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:19:11.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:19:11.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:11.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:11.999][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:12.000][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:12.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.002][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.004][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:19:12.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:19:12.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.009][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:12.010][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:12.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.012][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.014][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:19:12.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:19:12.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.019][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:19:12.020][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:12.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.022][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:19:12.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:12.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.028][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:12.030][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:12.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.032][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.034][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:12.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:19:12.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.038][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:12.040][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:12.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.042][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.044][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:12.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:19:12.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.048][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-03-01 16:19:12.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:12.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.053][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:12.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:12.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.058][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:12.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:19:12.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.063][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-03-01 16:19:12.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:12.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.068][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:12.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:12.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.072][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:12.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:19:12.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.077][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-03-01 16:19:12.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:12.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.082][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:12.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:12.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.087][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:12.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:19:12.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.091][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-03-01 16:19:12.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:12.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.096][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:12.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:12.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.101][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:12.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:19:12.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.106][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-03-01 16:19:12.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:12.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.111][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:12.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:12.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.115][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:12.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:19:12.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.120][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:12.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:12.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.125][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:12.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:12.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.130][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:12.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:12.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:12.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:12.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.139][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:12.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:19:12.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:12.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:12.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:12.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:12.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:12.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:12.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:12.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:12.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:12.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:12.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:12.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:12.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:12.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:12.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:12.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:12.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:19:12.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:19:12.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:19:12.187][self$createEntryFromContent] Accession numbers: 2, 65124.
biodb.TRACE[2025-03-01 16:19:12.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-01 16:19:12.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-01 16:19:12.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:19:12.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:19:12.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:19:12.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:19:12.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-01 16:19:12.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-01 16:19:12.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:19:12.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:19:12.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:19:12.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:19:12.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-01 16:19:12.232][biodb::testThat]
biodb.INFO [2025-03-01 16:19:12.234][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-01 16:19:12.235][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:19:12.236][biodb::testThat]
biodb.TRACE[2025-03-01 16:19:12.239][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:12.241][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:12.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.243][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:19:12.245][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.TRACE[2025-03-01 16:19:12.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:12.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:12.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:12.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:12.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:12.278][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:12.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:12.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:12.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:19:12.285][function(conn, opt)] With value "(2-acetyloxy-3-carboxypropyl)-trimethylazanium".
biodb.DEBUG[2025-03-01 16:19:12.292][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[2025-03-01 16:19:12.295][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:19:12.297][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0c7e343368bb974cc0f019187ff4a141".
biodb.TRACE[2025-03-01 16:19:12.299][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:19:34.936][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/0c7e343368bb974cc0f019187ff4a141.content".
biodb.DEBUG[2025-03-01 16:19:34.939][function(conn, opt)] With found IDs [5]: "87229113, 25217148, 450343, 450342, 2".
biodb.TRACE[2025-03-01 16:19:34.957][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:34.959][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:19:34.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:34.961][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:34.962][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:34.964][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:19:34.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:34.966][ef$get] fields variable is a list.
biodb.INFO [2025-03-01 16:19:34.972][biodb::testThat]
biodb.INFO [2025-03-01 16:19:34.973][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-01 16:19:34.974][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:19:34.976][biodb::testThat]
biodb.TRACE[2025-03-01 16:19:34.990][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:34.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:34.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:34.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:34.995][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:34.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:34.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:34.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:35.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:19:35.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:19:35.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:35.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:19:35.045][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[2025-03-01 16:19:35.049][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:19:35.050][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0c7e343368bb974cc0f019187ff4a141".
biodb.TRACE[2025-03-01 16:19:35.052][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:19:35.054][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/0c7e343368bb974cc0f019187ff4a141.content".
biodb.INFO [2025-03-01 16:19:35.076][biodb::testThat]
biodb.INFO [2025-03-01 16:19:35.078][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-01 16:19:35.079][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:19:35.080][biodb::testThat]
biodb.TRACE[2025-03-01 16:19:35.092][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:19:35.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:19:35.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:35.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:35.097][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:19:35.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:19:35.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:35.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:35.102][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:19:35.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:19:35.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:35.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:35.107][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:19:35.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:19:35.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:35.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:35.112][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:19:35.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:19:35.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:35.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:35.117][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:19:35.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:19:35.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:35.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:35.122][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:19:35.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:19:35.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:35.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:35.128][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:19:35.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:19:35.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:35.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:35.133][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:19:35.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:19:35.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:35.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:35.138][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:19:35.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:19:35.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:35.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:35.142][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:19:35.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:19:35.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:35.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:35.147][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:19:35.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:19:35.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:35.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:35.152][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:19:35.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:19:35.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:35.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:19:35.157][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:19:35.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:19:35.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:19:35.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-01 16:19:35.169][biodb::testThat]
biodb.INFO [2025-03-01 16:19:35.170][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-01 16:19:35.172][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:19:35.173][biodb::testThat]
biodb.INFO [2025-03-01 16:19:35.184][biodb::testThat]
biodb.INFO [2025-03-01 16:19:35.185][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-01 16:19:35.186][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:19:35.187][biodb::testThat]
biodb.INFO [2025-03-01 16:19:35.199][biodb::testThat]
biodb.INFO [2025-03-01 16:19:35.200][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-01 16:19:35.201][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:19:35.203][biodb::testThat]
biodb.DEBUG[2025-03-01 16:19:35.207][function(conn, opt)] Trying to download "https://pubchem.ncbi.nlm.nih.gov/compound/2".
biodb.DEBUG[2025-03-01 16:19:46.256][getUrlContent] Use base::url() for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/compound/2.
biodb.INFO [2025-03-01 16:19:57.357][biodb::testThat]
biodb.INFO [2025-03-01 16:19:57.358][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-01 16:19:57.359][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:19:57.360][biodb::testThat]
biodb.DEBUG[2025-03-01 16:20:08.421][getUrlContent] Use base::url() for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=2&t=l.
biodb.TRACE[2025-03-01 16:20:19.489][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:20:19.490][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:20:19.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:19.493][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:19.494][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:19.495][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:19.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:19.497][ef$get] fields variable is a list.
biodb.INFO [2025-03-01 16:20:19.500][biodb::testThat]
biodb.INFO [2025-03-01 16:20:19.501][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-03-01 16:20:19.502][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:20:19.503][biodb::testThat]
biodb.TRACE[2025-03-01 16:20:19.518][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:20:19.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:20:19.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:19.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:19.523][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:20:19.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:20:19.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:19.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:19.528][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:20:19.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:20:19.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:19.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:20:19.633][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[2025-03-01 16:20:19.637][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:20:19.638][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0c7e343368bb974cc0f019187ff4a141".
biodb.TRACE[2025-03-01 16:20:19.640][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:20:19.642][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/0c7e343368bb974cc0f019187ff4a141.content".
biodb.DEBUG[2025-03-01 16:20:19.710][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[2025-03-01 16:20:19.714][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:20:19.715][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0c7e343368bb974cc0f019187ff4a141".
biodb.TRACE[2025-03-01 16:20:19.717][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:20:19.719][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/0c7e343368bb974cc0f019187ff4a141.content".
biodb.TRACE[2025-03-01 16:20:19.737][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-01 16:20:19.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-01 16:20:19.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:19.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:19.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:19.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:19.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:19.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:19.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:19.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:19.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:19.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:19.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:19.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:19.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:19.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:19.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:19.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:19.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:19.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:19.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:19.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:19.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:19.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:20:19.779][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[2025-03-01 16:20:19.782][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:20:19.784][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2616ca37a6f6e1bc281f8c51bc53ce81".
biodb.TRACE[2025-03-01 16:20:19.785][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:20:22.671][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/2616ca37a6f6e1bc281f8c51bc53ce81.content".
biodb.DEBUG[2025-03-01 16:20:22.690][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[2025-03-01 16:20:22.694][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:20:22.696][cch$loadFileContent] Trying to load 1 files from cache: [1]: "43af01c58cfaf2fe3448c11004a21986".
biodb.TRACE[2025-03-01 16:20:22.697][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:20:22.958][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/43af01c58cfaf2fe3448c11004a21986.content".
biodb.DEBUG[2025-03-01 16:20:23.262][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[2025-03-01 16:20:23.266][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:20:23.267][cch$loadFileContent] Trying to load 1 files from cache: [1]: "5a651e56a091cb06291b388106735d55".
biodb.TRACE[2025-03-01 16:20:23.269][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:20:24.538][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/5a651e56a091cb06291b388106735d55.content".
biodb.DEBUG[2025-03-01 16:20:24.566][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[2025-03-01 16:20:24.570][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:20:24.571][cch$loadFileContent] Trying to load 1 files from cache: [1]: "d3d0da2755d093596dae584b7698bc73".
biodb.TRACE[2025-03-01 16:20:24.573][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:20:27.298][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/d3d0da2755d093596dae584b7698bc73.content".
biodb.TRACE[2025-03-01 16:20:27.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:27.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:27.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:27.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:27.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:27.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:27.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:27.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:27.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:27.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:27.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:27.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:27.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:27.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:27.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:27.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:27.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:27.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:27.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:27.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:20:27.363][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[2025-03-01 16:20:27.367][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:20:27.369][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1384af38a786fc6768cd7f1e796d96ab".
biodb.TRACE[2025-03-01 16:20:27.370][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:20:27.461][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/1384af38a786fc6768cd7f1e796d96ab.content".
biodb.DEBUG[2025-03-01 16:20:27.480][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[2025-03-01 16:20:27.484][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:20:27.486][cch$loadFileContent] Trying to load 1 files from cache: [1]: "983d3a3af3901d23b5d919d379c6bd32".
biodb.TRACE[2025-03-01 16:20:27.487][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:20:28.313][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/983d3a3af3901d23b5d919d379c6bd32.content".
biodb.DEBUG[2025-03-01 16:20:28.334][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[2025-03-01 16:20:28.338][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:20:28.340][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9a9be2efcff8c77fef3b8a87f25b444".
biodb.TRACE[2025-03-01 16:20:28.341][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:20:34.430][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/b9a9be2efcff8c77fef3b8a87f25b444.content".
biodb.DEBUG[2025-03-01 16:20:34.460][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[2025-03-01 16:20:34.463][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:20:34.465][cch$loadFileContent] Trying to load 1 files from cache: [1]: "6d4e46c6f0a021fc6e92911d60537192".
biodb.TRACE[2025-03-01 16:20:34.467][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:20:35.719][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/6d4e46c6f0a021fc6e92911d60537192.content".
biodb.TRACE[2025-03-01 16:20:35.743][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-01 16:20:35.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-01 16:20:35.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:35.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-01 16:20:35.759][biodb::testThat]
biodb.INFO [2025-03-01 16:20:35.760][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-01 16:20:35.761][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:20:35.762][biodb::testThat]
biodb.TRACE[2025-03-01 16:20:35.766][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-01 16:20:35.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-01 16:20:35.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:35.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:35.771][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-01 16:20:35.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-01 16:20:35.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:35.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:35.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:35.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:35.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:35.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:35.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:35.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:35.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:35.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:35.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:35.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:35.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:35.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:35.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:35.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:35.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:35.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:35.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:20:35.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:20:35.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:20:35.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:20:35.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:20:35.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:20:35.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:20:35.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:20:35.837][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[2025-03-01 16:20:35.840][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:20:35.842][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2616ca37a6f6e1bc281f8c51bc53ce81".
biodb.TRACE[2025-03-01 16:20:35.844][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:20:35.846][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/2616ca37a6f6e1bc281f8c51bc53ce81.content".
biodb.DEBUG[2025-03-01 16:20:35.848][private$loadEntries] Creating entries from ids [3]: "172649379, 172631573, 172608227".
biodb.DEBUG[2025-03-01 16:20:35.849][conn$getEntryContent] Get PubChem Compound entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-01 16:20:35.851][cch$loadFileContent] Trying to load 3 files from cache: [3]: "172649379, 172631573, 172608227".
biodb.TRACE[2025-03-01 16:20:35.853][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2025-03-01 16:20:40.294][loadFileContents] Loaded 3 files from cache: [3]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/172649379.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/172631573.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/172608227.xml".
biodb.DEBUG[2025-03-01 16:20:40.296][conn$getEntryContent] 3 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:20:40.298][self$createEntryFromContent] Creating PubChem Compound entries from 3 content(s).
biodb.DEBUG[2025-03-01 16:20:40.299][self$createEntryFromContent] Parsing 3 PubChem Compound entries.
biodb.DEBUG[2025-03-01 16:20:40.301][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:20:40.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:20:40.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:20:40.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:20:40.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:20:40.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:20:40.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:20:40.316][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:40.318][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:40.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.320][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:40.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:40.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.327][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.328][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.330][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.332][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.337][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:40.338][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:40.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.340][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.342][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:40.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:40.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.347][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.348][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.350][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.352][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.356][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.358][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.360][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.361][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.366][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.367][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.370][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.371][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.376][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:20:40.377][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:40.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.379][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.381][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:20:40.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:40.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.386][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:20:40.387][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:20:40.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.389][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.391][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:20:40.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:20:40.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.396][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:20:40.397][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:20:40.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.399][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:20:40.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:20:40.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.405][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:20:40.407][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:20:40.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.409][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:20:40.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:20:40.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.415][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:20:40.416][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:20:40.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.419][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.420][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:20:40.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:20:40.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.425][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:20:40.426][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:40.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.429][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:20:40.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:40.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.435][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:20:40.436][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:20:40.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.438][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.440][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:20:40.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:20:40.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.445][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:20:40.446][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:20:40.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.448][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.450][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:20:40.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:20:40.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.455][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-03-01 16:20:40.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.459][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.464][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.469][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-03-01 16:20:40.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.474][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.478][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.483][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-03-01 16:20:40.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.488][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.492][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.497][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-03-01 16:20:40.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.502][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.507][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.511][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-03-01 16:20:40.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:40.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.516][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:40.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:40.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.521][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:40.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:40.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.526][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:20:40.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:20:40.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.759][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:40.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:40.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.763][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:40.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:40.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:40.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:40.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.772][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:40.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:40.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:40.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:40.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:40.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:40.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:40.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:40.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:20:40.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:20:40.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:20:40.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:20:40.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:20:40.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:20:40.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:20:40.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:20:40.805][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:40.807][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:40.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.809][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:40.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:40.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.815][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.816][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.818][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.820][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.825][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:40.826][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:40.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.828][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.829][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:40.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:40.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.834][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.835][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.837][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.839][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.844][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.845][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.847][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.849][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.853][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.854][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.857][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.858][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.863][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:20:40.864][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:40.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.866][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.868][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:20:40.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:40.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.872][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:20:40.874][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:20:40.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.876][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.877][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:20:40.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:20:40.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.882][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:20:40.883][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:20:40.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.885][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.887][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:20:40.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:20:40.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.892][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:20:40.893][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:20:40.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.895][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.896][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:20:40.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:20:40.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.901][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:20:40.902][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:20:40.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.904][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.906][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:20:40.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:20:40.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.911][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:20:40.912][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:40.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.914][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:20:40.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:40.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.920][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:20:40.921][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:20:40.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.924][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.925][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:20:40.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:20:40.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.930][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:20:40.931][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:20:40.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.933][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.935][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:20:40.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:20:40.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.939][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-03-01 16:20:40.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.944][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.949][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:40.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.953][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-03-01 16:20:40.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.958][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.963][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:40.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.967][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-03-01 16:20:40.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.972][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.977][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:40.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.981][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-03-01 16:20:40.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.986][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.991][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:40.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:40.995][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-03-01 16:20:40.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:40.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:40.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.000][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:41.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:41.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.004][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:41.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:41.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.009][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:20:41.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:20:41.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.014][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.018][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.027][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:20:41.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:20:41.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:20:41.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:20:41.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:20:41.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:20:41.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:20:41.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:20:41.061][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.062][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.065][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.071][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:41.072][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:41.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.074][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.076][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:41.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:41.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.080][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:41.082][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:41.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.084][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.085][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:41.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:41.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.090][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:41.091][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:41.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.093][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.095][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:41.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:41.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.100][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:41.101][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:41.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.103][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.105][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:41.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:41.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.109][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:41.111][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:41.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.113][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.115][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:41.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:41.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.119][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:20:41.120][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:41.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.123][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.124][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:20:41.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:20:41.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.129][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:20:41.130][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:20:41.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.133][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:20:41.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:20:41.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.139][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:20:41.140][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:20:41.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.142][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.144][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:20:41.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:20:41.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.149][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:20:41.150][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:20:41.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.152][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:20:41.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:20:41.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.159][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:20:41.160][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:20:41.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.162][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.163][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:20:41.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:20:41.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.168][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:20:41.169][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:41.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.172][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:20:41.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:20:41.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.178][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:20:41.179][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:20:41.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.181][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.183][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:20:41.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:20:41.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.188][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:20:41.189][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:20:41.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.191][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.193][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:20:41.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:20:41.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.198][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-03-01 16:20:41.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:41.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.202][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:41.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:41.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.207][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:41.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:20:41.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.217][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-03-01 16:20:41.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:41.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.221][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:41.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:41.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.226][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:41.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:20:41.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.231][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-03-01 16:20:41.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:41.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.235][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:41.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:41.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.240][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:41.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:20:41.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.244][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-03-01 16:20:41.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:41.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.249][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:41.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:41.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.254][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:41.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:20:41.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.258][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-03-01 16:20:41.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:41.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.263][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:41.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:41.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.267][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:41.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:20:41.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:20:41.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:20:41.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.277][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.281][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.290][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:20:41.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:20:41.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:20:41.352][self$createEntryFromContent] Accession numbers: 172649379, 172631573, 172608227.
biodb.DEBUG[2025-03-01 16:20:41.353][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-01 16:20:41.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:20:41.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:20:41.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:20:41.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:20:41.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:20:41.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:20:41.366][FUN] Functions in observer BiodbConfig: [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[2025-03-01 16:20:41.367][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.372][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.377][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:20:41.378][private$selectFields]
biodb.TRACE[2025-03-01 16:20:41.379][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-01 16:20:41.380][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-01 16:20:41.381][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:20:41.382][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.383][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.385][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.387][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.388][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.390][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.391][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:20:41.392][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:20:41.393][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.395][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.397][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.398][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-03-01 16:20:41.399][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.404][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.408][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.420][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [172649379].
biodb.DEBUG[2025-03-01 16:20:41.421][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:20:41.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:20:41.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:20:41.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:20:41.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:20:41.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:20:41.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:20:41.434][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.439][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.444][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:20:41.445][private$selectFields]
biodb.TRACE[2025-03-01 16:20:41.446][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-01 16:20:41.447][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-01 16:20:41.448][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:20:41.449][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.450][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.453][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.454][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.455][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.457][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.458][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:20:41.459][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:20:41.461][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.462][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.464][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.465][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-03-01 16:20:41.466][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.471][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.475][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.480][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [172631573].
biodb.DEBUG[2025-03-01 16:20:41.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:20:41.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:20:41.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:20:41.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:20:41.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:20:41.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:20:41.493][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.TRACE[2025-03-01 16:20:41.495][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.499][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.504][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:20:41.505][private$selectFields]
biodb.TRACE[2025-03-01 16:20:41.506][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-01 16:20:41.507][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-01 16:20:41.508][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:20:41.509][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.511][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.513][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.514][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.515][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.517][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.518][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:20:41.520][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:20:41.521][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.522][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.524][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.525][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-03-01 16:20:41.526][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.531][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.536][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:20:41.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:20:41.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:20:41.540][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [172608227].
biodb.DEBUG[2025-03-01 16:20:41.542][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-01 16:20:41.543][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.DEBUG[2025-03-01 16:20:41.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:20:41.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:20:41.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:20:41.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:20:41.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:20:41.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:20:41.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:20:41.564][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[2025-03-01 16:20:41.568][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:20:41.569][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:20:41.571][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:20:52.620][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:20:52.622][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:20:52.624][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:20:52.625][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:21:03.679][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:21:03.681][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:21:03.682][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:21:03.685][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:21:14.730][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:21:14.731][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:21:14.734][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:21:14.735][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:21:25.783][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:21:25.784][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:21:25.785][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:21:25.787][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:21:36.832][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:21:36.834][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:21:36.836][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:21:36.838][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:21:47.886][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:21:47.888][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:21:47.890][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:21:47.891][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:21:58.937][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:21:58.939][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:21:58.940][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:21:58.942][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:22:09.990][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:22:09.992][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:22:09.993][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:22:09.995][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:22:21.040][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:22:21.042][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:22:21.044][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:22:21.045][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:22:32.092][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:22:32.094][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:22:32.096][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:22:32.099][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:22:43.142][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:22:43.143][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:22:43.146][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:22:43.148][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:22:54.194][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:22:54.196][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:22:54.197][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:22:54.199][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:23:05.260][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:23:05.261][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:23:05.263][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:23:05.265][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:23:16.324][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:23:16.326][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:23:16.328][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:23:16.330][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:23:27.378][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:23:27.380][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:23:27.382][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:23:27.383][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:23:38.432][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:23:38.433][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:23:38.435][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:23:38.437][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:23:49.482][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:23:49.484][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:23:49.486][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:23:49.488][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:23:55.062][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:23:55.064][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:23:55.065][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:23:55.067][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:23:55.074][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:23:55.075][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:23:55.077][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:23:55.079][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:23:55.083][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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 [2025-03-01 16:23:55.185][biodb::testThat]
biodb.INFO [2025-03-01 16:23:55.186][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-01 16:23:55.188][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:23:55.189][biodb::testThat]
biodb.TRACE[2025-03-01 16:23:55.194][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-01 16:23:55.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-01 16:23:55.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:55.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:55.200][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-01 16:23:55.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-01 16:23:55.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:55.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:55.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:55.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:55.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:55.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:55.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:55.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:55.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:55.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:55.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:55.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:55.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:55.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:55.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:55.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:55.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:55.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:55.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:23:55.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:23:55.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:23:55.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:23:55.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:23:55.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:23:55.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:23:55.318][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.DEBUG[2025-03-01 16:23:55.327][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[2025-03-01 16:23:55.331][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:23:55.333][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aa9cb23a1eb4b2596e7c242b1c35f744".
biodb.TRACE[2025-03-01 16:23:55.335][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:23:55.674][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/aa9cb23a1eb4b2596e7c242b1c35f744.content".
biodb.DEBUG[2025-03-01 16:23:55.677][private$loadEntries] Creating entries from ids [1]: "172574413".
biodb.DEBUG[2025-03-01 16:23:55.678][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-01 16:23:55.680][cch$loadFileContent] Trying to load 1 files from cache: [1]: "172574413".
biodb.TRACE[2025-03-01 16:23:55.682][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:23:56.444][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/172574413.xml".
biodb.DEBUG[2025-03-01 16:23:56.446][conn$getEntryContent] 1 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:23:56.448][self$createEntryFromContent] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:23:56.450][self$createEntryFromContent] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-03-01 16:23:56.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:23:56.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:23:56.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:23:56.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:23:56.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:23:56.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:23:56.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:23:56.470][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:23:56.471][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:23:56.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.474][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:23:56.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:23:56.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.481][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:23:56.483][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:23:56.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.485][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.487][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:23:56.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:23:56.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.492][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:23:56.494][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:23:56.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.496][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:23:56.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:23:56.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.504][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:23:56.505][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:23:56.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.507][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.509][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:23:56.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:23:56.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.515][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:23:56.516][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:23:56.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.519][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.521][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:23:56.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:23:56.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.526][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:23:56.527][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:23:56.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.530][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.532][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:23:56.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:23:56.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.537][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:23:56.539][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:23:56.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.541][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.543][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-03-01 16:23:56.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:23:56.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.548][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:23:56.550][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:23:56.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.552][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.554][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:23:56.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:23:56.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.560][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:23:56.561][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:23:56.562][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.564][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:23:56.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:23:56.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.571][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:23:56.572][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:23:56.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.575][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:23:56.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:23:56.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.582][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:23:56.583][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:23:56.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.586][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.588][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:23:56.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:23:56.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.593][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:23:56.594][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:56.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.597][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.599][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-03-01 16:23:56.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:23:56.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.604][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:23:56.606][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:23:56.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.608][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.610][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:23:56.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:23:56.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.615][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:23:56.617][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:23:56.618][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.619][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.621][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:23:56.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:23:56.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.626][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-03-01 16:23:56.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:23:56.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.630][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:23:56.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:23:56.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.635][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:23:56.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:23:56.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.640][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-03-01 16:23:56.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:23:56.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.645][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:23:56.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:23:56.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.650][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:23:56.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:23:56.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.655][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-03-01 16:23:56.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:23:56.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.660][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:23:56.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:23:56.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.664][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:23:56.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:23:56.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.669][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-03-01 16:23:56.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:23:56.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.674][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:23:56.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:23:56.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.679][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:23:56.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:23:56.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.684][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-03-01 16:23:56.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:23:56.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.688][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:23:56.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:23:56.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.693][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:23:56.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:23:56.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:23:56.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:23:56.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.709][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.713][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:23:56.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:23:56.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.723][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:23:56.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:23:56.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:23:56.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:23:56.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:23:56.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:23:56.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:23:56.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:23:56.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:23:56.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:23:56.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:23:56.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:23:56.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:23:56.756][self$createEntryFromContent] Accession numbers: 172574413.
biodb.DEBUG[2025-03-01 16:23:56.776][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-01 16:23:56.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:23:56.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:23:56.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:23:56.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:23:56.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:23:56.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:23:56.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:23:56.819][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.823][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.844][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:23:56.846][private$selectFields]
biodb.TRACE[2025-03-01 16:23:56.847][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-01 16:23:56.848][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-01 16:23:56.849][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:23:56.850][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.852][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.854][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.855][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.856][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.858][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.859][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:23:56.868][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:23:56.870][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.871][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.873][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.874][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-03-01 16:23:56.875][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.880][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.885][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.890][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [172631573].
biodb.DEBUG[2025-03-01 16:23:56.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:23:56.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:23:56.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:23:56.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:23:56.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:23:56.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:23:56.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:23:56.904][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.909][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.913][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:23:56.914][private$selectFields]
biodb.TRACE[2025-03-01 16:23:56.916][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-01 16:23:56.917][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-01 16:23:56.918][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:23:56.919][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.920][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.922][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.924][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.925][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.926][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.927][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.928][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:23:56.929][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:23:56.930][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.932][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.934][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.935][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-03-01 16:23:56.936][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.941][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.946][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.951][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [172608227].
biodb.DEBUG[2025-03-01 16:23:56.952][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:23:56.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:23:56.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:23:56.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:23:56.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:23:56.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:23:56.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:23:56.965][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.970][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.974][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:23:56.975][private$selectFields]
biodb.TRACE[2025-03-01 16:23:56.977][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-01 16:23:56.978][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-01 16:23:56.979][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:23:56.980][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.981][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.983][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.985][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.986][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.988][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.989][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:23:56.990][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:23:56.991][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.993][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:56.995][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:56.996][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-03-01 16:23:56.997][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:56.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:57.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:57.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:57.002][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:57.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:57.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:57.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:57.007][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:57.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:23:57.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:23:57.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:23:57.012][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [172574413].
biodb.DEBUG[2025-03-01 16:23:57.013][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-01 16:23:57.014][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.DEBUG[2025-03-01 16:23:57.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:23:57.017][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:23:57.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:23:57.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:23:57.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:23:57.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:23:57.028][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[2025-03-01 16:23:57.036][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[2025-03-01 16:23:57.183][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:23:57.184][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:23:57.187][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:08.234][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:08.236][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:08.238][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:08.239][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:19.395][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:19.397][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:19.398][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:19.401][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:30.446][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:30.447][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:30.449][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:30.451][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:31.244][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:31.246][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:31.247][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:31.249][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:31.255][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:31.257][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:31.259][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:31.261][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:31.265][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:31.266][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:31.268][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:31.270][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:31.276][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:31.277][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:31.279][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:31.281][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:31.284][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:31.286][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:31.287][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:31.295][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:31.302][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:31.303][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:31.305][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:31.307][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:31.311][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:31.312][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:31.313][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:31.315][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:31.321][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:31.322][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:31.323][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:31.325][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:31.329][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:31.330][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:31.331][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:31.333][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:31.338][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:31.340][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:31.341][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:31.343][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:31.346][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:31.347][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:31.348][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:24:31.350][rule$waitAsNeeded] Wait 0.898831 second(s).
biodb.TRACE[2025-03-01 16:24:32.261][private$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[2025-03-01 16:24:32.267][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:32.268][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:32.270][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:32.272][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:24:32.276][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:24:32.277][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:32.279][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:32.281][private$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[2025-03-01 16:24:32.287][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:32.288][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:32.290][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:32.291][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:24:32.295][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:24:32.296][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:32.297][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:32.299][private$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[2025-03-01 16:24:32.305][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:32.306][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:32.308][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:32.309][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:24:32.313][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.INFO [2025-03-01 16:24:32.330][biodb::testThat]
biodb.INFO [2025-03-01 16:24:32.331][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-01 16:24:32.333][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:24:32.334][biodb::testThat]
biodb.TRACE[2025-03-01 16:24:32.337][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-01 16:24:32.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-01 16:24:32.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.342][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-01 16:24:32.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-01 16:24:32.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:32.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:24:32.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:24:32.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:24:32.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:24:32.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:24:32.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:24:32.400][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:24:32.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:24:32.407][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.23:204.25[MolecularWeight]&retmax=3".
biodb.DEBUG[2025-03-01 16:24:32.411][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:24:32.412][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2616ca37a6f6e1bc281f8c51bc53ce81".
biodb.TRACE[2025-03-01 16:24:32.414][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:24:32.800][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/2616ca37a6f6e1bc281f8c51bc53ce81.content".
biodb.DEBUG[2025-03-01 16:24:32.803][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-01 16:24:32.805][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:24:32.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:24:32.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:24:32.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:24:32.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:24:32.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:24:32.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:24:32.818][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.823][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.827][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:24:32.829][private$selectFields]
biodb.TRACE[2025-03-01 16:24:32.830][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-01 16:24:32.831][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-01 16:24:32.832][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:24:32.833][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.834][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.836][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.838][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.839][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.841][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.842][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:24:32.843][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:24:32.844][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.846][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.848][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.849][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-03-01 16:24:32.850][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.855][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.859][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.864][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [172649379].
biodb.DEBUG[2025-03-01 16:24:32.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:24:32.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:24:32.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:24:32.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:24:32.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:24:32.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:24:32.878][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.TRACE[2025-03-01 16:24:32.879][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.884][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.888][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:24:32.889][private$selectFields]
biodb.TRACE[2025-03-01 16:24:32.891][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-01 16:24:32.892][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-01 16:24:32.893][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:24:32.894][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.895][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.897][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.899][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.900][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.903][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:24:32.904][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:24:32.905][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.907][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.909][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.910][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-03-01 16:24:32.911][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.916][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.920][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.925][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [172631573].
biodb.DEBUG[2025-03-01 16:24:32.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:24:32.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:24:32.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:24:32.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:24:32.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:24:32.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:24:32.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:24:32.940][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.945][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.949][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:24:32.951][private$selectFields]
biodb.TRACE[2025-03-01 16:24:32.952][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-01 16:24:32.953][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-01 16:24:32.954][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:24:32.955][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.956][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.959][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.960][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.961][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.963][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.964][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:24:32.965][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2025-03-01 16:24:32.967][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.968][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.970][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.971][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2025-03-01 16:24:32.972][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.977][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.982][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:32.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:32.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:32.987][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [172608227].
biodb.DEBUG[2025-03-01 16:24:32.988][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-01 16:24:32.989][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.DEBUG[2025-03-01 16:24:32.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:24:32.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:24:32.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:24:33.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:24:33.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:24:33.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:24:33.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:24:33.010][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18:226.2[MolecularWeight]&retmax=3".
biodb.DEBUG[2025-03-01 16:24:33.013][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:33.014][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:33.016][private$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[2025-03-01 16:24:33.022][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:33.023][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:33.025][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:33.027][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:24:33.030][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:24:33.031][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:33.033][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:33.035][private$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[2025-03-01 16:24:33.041][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:33.042][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:33.043][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:33.045][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:24:33.049][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:24:33.050][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:33.051][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:24:33.052][rule$waitAsNeeded] Wait 0.207983 second(s).
biodb.TRACE[2025-03-01 16:24:33.263][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:33.269][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:33.270][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:33.272][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:33.274][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:33.278][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:33.279][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:33.280][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:33.282][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:33.288][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:33.289][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:33.291][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:33.292][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:33.296][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:33.297][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:33.298][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:33.300][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:33.306][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:33.307][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:33.309][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:33.311][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:33.314][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:33.321][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:33.322][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:24:33.323][rule$waitAsNeeded] Wait 0.692733 second(s).
biodb.TRACE[2025-03-01 16:24:34.030][private$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[2025-03-01 16:24:34.037][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:34.038][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:34.040][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:34.041][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:24:34.045][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:24:34.046][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:34.047][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:34.049][private$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[2025-03-01 16:24:34.055][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:34.056][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:34.058][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:34.059][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:24:34.063][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:24:34.064][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:34.065][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:24:34.067][rule$waitAsNeeded] Wait 0.195472 second(s).
biodb.TRACE[2025-03-01 16:24:34.265][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:34.273][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:34.274][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:34.275][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:34.277][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:34.391][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:34.392][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:34.394][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:34.396][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:34.402][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:34.403][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:34.405][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:34.406][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:34.410][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:34.411][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:34.412][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:34.414][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:34.420][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:34.421][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:34.422][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:34.424][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:34.427][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:34.444][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:34.445][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:34.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:34.447][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:34.448][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.450][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:34.452][ef$get] fields variable is a list.
biodb.INFO [2025-03-01 16:24:34.454][biodb::testThat]
biodb.INFO [2025-03-01 16:24:34.455][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-03-01 16:24:34.456][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:24:34.457][biodb::testThat]
biodb.TRACE[2025-03-01 16:24:34.461][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-01 16:24:34.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-01 16:24:34.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:34.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:34.466][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-01 16:24:34.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-01 16:24:34.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:34.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:34.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:34.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:34.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:34.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:34.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:34.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:34.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:34.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:34.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:34.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:34.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:34.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:34.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:34.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:34.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:34.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:34.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:24:34.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:24:34.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:24:34.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:24:34.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:24:34.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:24:34.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:24:34.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:24:34.529][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[2025-03-01 16:24:34.532][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:34.533][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:24:34.535][rule$waitAsNeeded] Wait 0.49452 second(s).
biodb.TRACE[2025-03-01 16:24:35.047][private$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[2025-03-01 16:24:35.054][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:35.055][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:35.057][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:35.058][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:24:35.062][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:24:35.064][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:35.065][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:35.067][private$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[2025-03-01 16:24:35.073][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:35.074][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:35.075][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:35.077][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:24:35.080][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:24:35.082][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:35.083][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:24:35.084][rule$waitAsNeeded] Wait 0.179832 second(s).
biodb.TRACE[2025-03-01 16:24:35.267][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:35.274][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:35.275][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:35.277][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:35.279][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:35.283][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:35.284][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:35.285][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:24:35.287][rule$waitAsNeeded] Wait 0.108935 second(s).
biodb.TRACE[2025-03-01 16:24:35.407][private$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[2025-03-01 16:24:35.414][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:35.415][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:35.417][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:35.418][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:24:35.422][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:24:35.423][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:35.424][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:35.426][private$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[2025-03-01 16:24:35.432][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:35.433][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:35.435][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:35.436][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:24:35.440][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:24:35.441][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:35.442][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:24:35.443][rule$waitAsNeeded] Wait 0.60308 second(s).
biodb.TRACE[2025-03-01 16:24:36.065][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:42.941][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:42.942][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:42.944][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:42.945][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:43.062][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:43.064][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:43.065][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:43.067][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:43.073][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:43.074][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:43.076][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:43.077][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:43.081][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:43.082][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:43.084][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:43.086][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:43.091][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:43.092][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:43.094][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:43.096][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:43.099][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:43.101][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:43.102][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:43.104][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:43.109][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:43.110][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:43.112][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:43.114][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:43.118][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:43.119][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:43.120][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:43.122][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:43.128][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:43.129][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:43.130][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:43.132][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:43.136][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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 [2025-03-01 16:24:43.153][biodb::testThat]
biodb.INFO [2025-03-01 16:24:43.154][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-03-01 16:24:43.156][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:24:43.157][biodb::testThat]
biodb.TRACE[2025-03-01 16:24:43.160][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-01 16:24:43.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-01 16:24:43.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.165][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-01 16:24:43.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-01 16:24:43.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:24:43.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:24:43.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:24:43.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:24:43.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:24:43.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:24:43.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:24:43.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:24:43.229][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[2025-03-01 16:24:43.232][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:24:43.234][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2616ca37a6f6e1bc281f8c51bc53ce81".
biodb.TRACE[2025-03-01 16:24:43.236][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:24:43.238][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/2616ca37a6f6e1bc281f8c51bc53ce81.content".
biodb.DEBUG[2025-03-01 16:24:43.240][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-01 16:24:43.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:24:43.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:24:43.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:24:43.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:24:43.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:24:43.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:24:43.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:24:43.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:43.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:43.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:43.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:43.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.264][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.269][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.274][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.279][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.283][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.293][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.299][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.303][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.308][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.312][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.317][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:43.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:43.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.322][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:43.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:43.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:43.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:43.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.331][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:43.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:43.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.336][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.345][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:43.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:43.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.349][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:43.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:43.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.373][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:43.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:43.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.378][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:43.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:43.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.382][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.387][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.391][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.396][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.401][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.405][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.410][private$selectFields] Fields [16]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2025-03-01 16:24:43.411][private$selectFields]
biodb.TRACE[2025-03-01 16:24:43.412][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-01 16:24:43.413][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-01 16:24:43.414][private$selectFields] Fields [16]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2025-03-01 16:24:43.415][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:43.417][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:43.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.419][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.420][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.421][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.423][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.425][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.426][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.428][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.429][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.430][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.433][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.434][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.435][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.437][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.438][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.440][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.442][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.443][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:43.444][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:43.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.446][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.447][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:43.449][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:43.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.451][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.452][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.453][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.455][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.457][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:43.458][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:43.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.460][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.461][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.462][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.464][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.466][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.467][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.469][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.470][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:43.471][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:43.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.474][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.475][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.476][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.478][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.479][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.480][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.483][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.484][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.485][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.487][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.488][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:43.490][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:43.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.492][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.493][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.494][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.496][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.497][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.499][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.501][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.502][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.503][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.505][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.507][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.508][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.510][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.511][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.512][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.515][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.516][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:43.517][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:43.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.519][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.520][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:43.521][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:43.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.524][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.525][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.526][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.528][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.529][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:43.530][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:43.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.533][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.534][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.535][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.537][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.538][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.540][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.542][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.543][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:43.544][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:43.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.546][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.547][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.549][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.551][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.552][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.553][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.555][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.557][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.558][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.560][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.561][private$selectFields] Fields [16]: "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[2025-03-01 16:24:43.562][private$organizeFieldsByGroups] Fields [16]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2025-03-01 16:24:43.563][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:43.565][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:43.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.567][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.568][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.569][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.571][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.573][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.574][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.576][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.577][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.578][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.580][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.582][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.583][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.585][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.586][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.587][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.590][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.591][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:43.592][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:43.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.594][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.595][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:43.596][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:43.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.599][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.600][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.601][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.603][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.604][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:43.606][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:43.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.608][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.609][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.610][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.612][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.613][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.615][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.617][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.618][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:43.619][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:43.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.621][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.623][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.624][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.626][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.627][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.628][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.631][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.632][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.633][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.634][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.635][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.636][private$organizeFieldsByGroups] Groups [2]: "c("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", "molecular.mass", "monoisotopic.mass", "name", "ncbi.pubchem.comp.id", "smiles.canonical", "smiles.isomeric"), list()"
biodb.TRACE[2025-03-01 16:24:43.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:43.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:43.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:43.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:43.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:43.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:43.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.652][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.657][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.661][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.666][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.671][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.676][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.681][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.685][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.690][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.695][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.700][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.705][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.709][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.714][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.719][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.724][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:43.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:43.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.729][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:43.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:43.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.738][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:43.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:43.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:43.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:43.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.748][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:43.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:43.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:43.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:43.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.762][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.767][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.771][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:43.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:43.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.776][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:43.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:43.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.781][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:43.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:43.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:43.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:43.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.818][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:43.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:43.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.823][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:43.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:43.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.828][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.832][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.837][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:43.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.841][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.846][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.851][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:43.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.855][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.861][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.867][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:43.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.880][private$entriesToListOfDataframes] Entry converted to data frame: [1, 16]: [accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, ...] [172649379, 3-(4-pyrimidin-5-ylpyrazol-1-yl)propan-1-ol, 3-[4-(5-pyrimidinyl)-1-pyrazolyl]-1-propanol, 3-(4-pyrimidin-5-ylpyrazol-1-yl)propan-1-ol, 3-(4-pyrimidin-5-ylpyrazol-1-yl)propan-1-ol, ...].
biodb.DEBUG[2025-03-01 16:24:43.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:24:43.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:24:43.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:24:43.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:24:43.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:24:43.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:24:43.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:24:43.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:43.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:43.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:43.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:43.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.903][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.908][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:43.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.913][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.918][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:43.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.922][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.927][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:43.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.932][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.936][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:43.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.941][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.946][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:43.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.950][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:43.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:43.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.955][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:43.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:43.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.959][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:43.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:43.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:43.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:43.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.973][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:43.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.978][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:43.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:43.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.983][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:43.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:43.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.987][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.992][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:43.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:43.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:43.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:43.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.006][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:44.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:44.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.010][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:44.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:44.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.015][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.019][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.024][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.029][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.033][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.038][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.043][private$selectFields] Fields [16]: "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[2025-03-01 16:24:44.044][private$selectFields]
biodb.TRACE[2025-03-01 16:24:44.045][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-01 16:24:44.046][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-01 16:24:44.047][private$selectFields] Fields [16]: "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[2025-03-01 16:24:44.048][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:44.049][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:44.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.051][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.053][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.054][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.056][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.057][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.058][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.061][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.062][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.063][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.065][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.066][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.068][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.070][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.071][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.072][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.074][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.075][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:44.077][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:44.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.079][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.080][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:44.081][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:44.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.083][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.084][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.086][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.088][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.089][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:44.090][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:44.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.092][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.093][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.095][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.097][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.098][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.099][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.101][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.102][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:44.104][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:44.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.106][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.107][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.108][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.111][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.112][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.113][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.115][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.116][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.117][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.120][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.121][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:44.122][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:44.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.124][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.126][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.127][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.129][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.130][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.132][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.134][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.135][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.136][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.139][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.141][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.143][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.144][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.145][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.147][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.149][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:44.150][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:44.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.152][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.153][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:44.154][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:44.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.157][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.158][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.159][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.161][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.162][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:44.164][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:44.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.166][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.167][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.168][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.170][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.172][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.173][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.181][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:44.183][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:44.184][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.185][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.186][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.187][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.189][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.190][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.192][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.194][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.195][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.196][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.197][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.198][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.199][private$selectFields] Fields [16]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2025-03-01 16:24:44.201][private$organizeFieldsByGroups] Fields [16]: "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[2025-03-01 16:24:44.202][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:44.203][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:44.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.205][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.206][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.208][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.210][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.211][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.212][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.214][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.215][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.217][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.219][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.220][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.221][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.223][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.224][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.226][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.228][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.229][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:44.230][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:44.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.232][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.233][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:44.235][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:44.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.237][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.238][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.239][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.241][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.242][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:44.244][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:44.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.246][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.247][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.248][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.250][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.251][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.253][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.255][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.256][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:44.257][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:44.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.259][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.260][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.262][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.264][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.265][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.266][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.268][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.269][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.271][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.273][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.274][private$organizeFieldsByGroups] Groups [2]: "c("accession", "comp.iupac.name.allowed", "comp.iupac.name.cas", "comp.iupac.name.pref", "comp.iupac.name.syst", "comp.iupac.name.trad", "formula", "inchi", "inchikey", "logp", "molecular.mass", "monoisotopic.mass", "name", "ncbi.pubchem.comp.id", "smiles.canonical", "smiles.isomeric"), list()"
biodb.TRACE[2025-03-01 16:24:44.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:44.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:44.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:44.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:44.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:44.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:44.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.290][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.294][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.299][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.304][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.308][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.313][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.317][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.322][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.327][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.331][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.336][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.341][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.345][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.350][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.355][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.359][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:44.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:44.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.364][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:44.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:44.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.369][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:44.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:44.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.374][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:44.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:44.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.378][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:44.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:44.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.383][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:44.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:44.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.388][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.402][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:44.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:44.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.407][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:44.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:44.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.411][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:44.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:44.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.444][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:44.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:44.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:44.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:44.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:44.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:44.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.458][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.463][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.468][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.472][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.477][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.482][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.487][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.491][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.496][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.507][private$entriesToListOfDataframes] Entry converted to data frame: [1, 16]: [accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, ...] [172631573, 3-(2-ethyl-3-fluoro-5-methyl-phenyl)-4H-pyrazole, 3-(2-ethyl-3-fluoro-5-methylphenyl)-4H-pyrazole, 3-(2-ethyl-3-fluoro-5-methylphenyl)-4H-pyrazole, 3-(2-ethyl-3-fluoranyl-5-methyl-phenyl)-4H-pyrazole, ...].
biodb.DEBUG[2025-03-01 16:24:44.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:24:44.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:24:44.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:24:44.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:24:44.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:24:44.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:24:44.520][FUN] Functions in observer BiodbConfig: [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[2025-03-01 16:24:44.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:44.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:44.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:44.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:44.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.531][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.536][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.540][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.545][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.550][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.554][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.559][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.564][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.569][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.574][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.578][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:44.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:44.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.583][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:44.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:44.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:44.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:44.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.592][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:44.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:44.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.597][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.602][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.607][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:44.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:44.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.611][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:44.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:44.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.640][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:44.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:44.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.644][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:44.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:44.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.649][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.653][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.658][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.663][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.667][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.672][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.676][private$selectFields] Fields [16]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2025-03-01 16:24:44.678][private$selectFields]
biodb.TRACE[2025-03-01 16:24:44.679][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-01 16:24:44.680][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-01 16:24:44.681][private$selectFields] Fields [16]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2025-03-01 16:24:44.682][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:44.683][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:44.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.685][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.687][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.688][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.690][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.691][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.692][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.694][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.696][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.697][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.699][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.700][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.701][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.704][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.705][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.706][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.708][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.709][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:44.710][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:44.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.713][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.714][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:44.715][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:44.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.717][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.718][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.720][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.722][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.723][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:44.724][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:44.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.726][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.727][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.729][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.731][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.732][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.733][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.735][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.737][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:44.738][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:44.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.740][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.741][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.742][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.744][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.746][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.747][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.749][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.750][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.751][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.754][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.755][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:44.756][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:44.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.758][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.759][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.760][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.763][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.764][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.765][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.767][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.768][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.770][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.772][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.773][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.774][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.776][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.777][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.779][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.781][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.782][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:44.783][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:44.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.785][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.786][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:44.788][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:44.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.790][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.791][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.792][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.794][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.796][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:44.797][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:44.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.799][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.800][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.801][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.803][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.805][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.806][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.808][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.809][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:44.810][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:44.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.813][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.814][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.815][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.817][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.818][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.820][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.822][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.823][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.824][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.826][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.827][private$selectFields] Fields [16]: "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[2025-03-01 16:24:44.829][private$organizeFieldsByGroups] Fields [16]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2025-03-01 16:24:44.830][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:44.831][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:44.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.833][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.834][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.836][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.838][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.839][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.840][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.841][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.842][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.844][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.845][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.847][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.848][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.849][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.852][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.853][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.854][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.856][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.857][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:44.858][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:44.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.861][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.862][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:44.863][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:44.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.865][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.866][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.868][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:44.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.870][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.871][ef$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:44.872][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:44.873][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.874][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.876][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.877][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:44.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.879][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.880][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.881][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:44.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.884][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.885][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:44.886][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:44.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.888][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.889][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.890][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:44.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.893][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.894][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.895][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:44.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.897][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.898][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.900][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:44.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.903][private$organizeFieldsByGroups] Groups [2]: "c("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", "molecular.mass", "monoisotopic.mass", "name", "ncbi.pubchem.comp.id", "smiles.canonical", "smiles.isomeric"), list()"
biodb.TRACE[2025-03-01 16:24:44.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:44.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:44.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:44.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:44.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:24:44.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:24:44.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.919][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.923][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.928][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-03-01 16:24:44.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.933][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.937][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.942][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-03-01 16:24:44.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.947][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.951][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.956][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-03-01 16:24:44.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.961][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.965][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.970][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-01 16:24:44.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.975][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.979][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.984][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-01 16:24:44.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.989][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:44.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:44.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.993][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:44.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:44.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:44.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:44.998][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:24:44.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:24:45.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.003][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:45.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:45.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:45.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:45.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.012][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:24:45.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:24:45.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.017][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:45.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:45.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.022][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:45.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:45.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.027][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:24:45.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:24:45.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.031][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:45.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:45.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.036][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:45.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:45.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.041][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-03-01 16:24:45.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-03-01 16:24:45.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:45.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:45.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:45.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:45.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:45.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:24:45.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:45.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:45.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:45.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:45.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:45.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-01 16:24:45.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.080][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:45.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:45.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:45.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:45.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:24:45.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:24:45.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.094][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:45.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:45.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.098][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:45.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:45.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.103][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:45.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:24:45.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.108][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:45.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:45.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.112][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:45.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:45.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.117][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:45.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-03-01 16:24:45.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.122][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:45.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:45.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.127][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:45.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:45.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.131][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:45.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-03-01 16:24:45.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:24:45.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:24:45.143][private$entriesToListOfDataframes] Entry converted to data frame: [1, 16]: [accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, ...] [172608227, 4-ethyl-1-[(4-fluorophenyl)methyl]imidazole, 4-ethyl-1-[(4-fluorophenyl)methyl]imidazole, 4-ethyl-1-[(4-fluorophenyl)methyl]imidazole, 4-ethyl-1-[(4-fluorophenyl)methyl]imidazole, ...].
biodb.DEBUG[2025-03-01 16:24:45.144][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-01 16:24:45.145][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.DEBUG[2025-03-01 16:24:45.148][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:24:45.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:24:45.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:24:45.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:24:45.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:24:45.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:24:45.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:24:45.167][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[2025-03-01 16:24:45.170][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:45.171][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:45.173][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:45.179][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:45.181][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:45.182][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:45.184][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:45.188][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:45.189][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:45.190][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:45.192][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:45.198][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:45.199][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:45.201][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:45.202][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:45.206][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:45.207][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:45.208][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:45.210][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:45.216][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:45.217][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:45.219][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:45.220][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:45.224][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:45.225][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:45.226][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:45.228][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:45.234][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:45.235][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:45.236][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:45.238][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:45.242][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:45.243][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:45.244][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:24:45.246][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2025-03-01 16:24:45.251][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:45.252][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:45.254][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:45.256][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.INFO [2025-03-01 16:24:45.259][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). 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[2025-03-01 16:24:45.260][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:24:45.261][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-01 16:24:45.263][rule$waitAsNeeded] Wait 0.910351 second(s).
biodb.TRACE[2025-03-01 16:24:46.193][private$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[2025-03-01 16:24:57.244][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:24:57.246][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:24:57.248][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:24:57.250][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:25:08.298][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:25:08.300][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:25:08.301][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:25:08.303][private$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[2025-03-01 16:25:19.348][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:25:19.350][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:25:19.352][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:25:19.353][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:25:30.400][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:25:30.402][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:25:30.404][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:25:30.406][private$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[2025-03-01 16:25:41.466][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:25:41.467][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:25:41.469][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:25:41.471][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:25:52.534][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:25:52.536][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:25:52.537][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:25:52.539][private$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[2025-03-01 16:26:03.584][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:26:03.586][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:26:03.588][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:26:03.590][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:26:14.637][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.DEBUG[2025-03-01 16:26:14.639][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:26:14.640][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:26:14.643][private$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[2025-03-01 16:26:25.687][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2025-03-01 16:26:25.689][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-01 16:26:25.691][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-01 16:26:25.693][getBaseUrlRequestResult] Using base::url() 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 [2025-03-01 16:26:36.740][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3". Retrying connection to server...
biodb.INFO [2025-03-01 16:26:36.758][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-01 16:26:36.760][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.pubchem.comp from the request scheduler
biodb.INFO [2025-03-01 16:26:36.762][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2025-03-01 16:26:36.763][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-01 16:26:36.764][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:36.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:36.766][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:36.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:36.769][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:36.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-01 16:26:41.587][biodb::testContext]
biodb.INFO [2025-03-01 16:26:41.589][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:26:41.590][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2025-03-01 16:26:41.592][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:26:41.593][biodb::testContext]
biodb.INFO [2025-03-01 16:26:41.681][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:26:41.684][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-01 16:26:41.769][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:26:41.771][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-01 16:26:41.772][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-01 16:26:41.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.776][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-01 16:26:41.778][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-01 16:26:41.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.782][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-01 16:26:41.783][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-01 16:26:41.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.788][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-01 16:26:41.789][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-01 16:26:41.790][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-01 16:26:41.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.794][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-01 16:26:41.796][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-01 16:26:41.797][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-01 16:26:41.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.801][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-01 16:26:41.802][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-01 16:26:41.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.807][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-01 16:26:41.808][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-01 16:26:41.809][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-01 16:26:41.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.813][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-01 16:26:41.814][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-01 16:26:41.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.819][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-01 16:26:41.820][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-01 16:26:41.821][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-01 16:26:41.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.825][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:26:41.827][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-01 16:26:41.828][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-01 16:26:41.829][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-01 16:26:41.830][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-01 16:26:41.831][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-01 16:26:41.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.836][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-01 16:26:41.837][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-01 16:26:41.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.841][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-01 16:26:41.842][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-01 16:26:41.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.847][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-01 16:26:41.848][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-01 16:26:41.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.852][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-01 16:26:41.854][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-01 16:26:41.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.858][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-01 16:26:41.859][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-01 16:26:41.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.862][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[2025-03-01 16:26:41.864][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:26:41.865][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-01 16:26:41.868][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-01 16:26:41.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.873][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-01 16:26:41.874][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-01 16:26:41.875][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-01 16:26:41.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:41.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:41.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:41.880][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-01 16:26:41.882][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:41.884][self$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[2025-03-01 16:26:41.885][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:41.886][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:26:41.888][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:41.889][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:26:41.890][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:41.891][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:26:41.892][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:26:41.894][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:26:41.895][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:41.896][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-01 16:26:41.897][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:26:41.898][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:41.900][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:41.901][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:26:41.901][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:26:41.901][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:26:41.901][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:26:41.901][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:26:41.902][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:26:41.903][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:41.904][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:41.905][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:26:41.907][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:41.908][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:41.909][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:26:41.910][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:41.911][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:26:41.912][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:26:41.913][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:41.914][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:41.916][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-01 16:26:41.918][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:41.919][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:26:41.920][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:41.921][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:26:41.923][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:41.924][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:26:41.925][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:41.926][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:26:41.927][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:26:41.929][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:26:41.930][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:41.931][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-01 16:26:41.939][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:26:41.940][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:41.941][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:41.942][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:26:41.942][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:26:41.942][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:26:41.942][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:26:41.942][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:26:41.944][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:26:41.945][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:41.946][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:41.947][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:26:41.948][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:41.949][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:41.950][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:26:41.952][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:41.953][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:26:41.954][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:26:41.955][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:41.956][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:41.957][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-01 16:26:41.959][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:41.961][self$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[2025-03-01 16:26:41.962][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:41.963][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:26:41.964][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:41.965][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:26:41.966][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:41.968][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:26:41.969][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:26:41.970][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:26:41.971][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:41.972][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-01 16:26:41.973][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:26:41.975][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:41.976][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:41.977][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:41.978][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:26:41.979][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:41.980][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:41.981][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:26:41.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:41.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:41.985][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:26:41.986][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:41.987][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:26:41.988][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:26:41.989][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:41.991][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:41.992][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-01 16:26:41.994][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:41.995][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:26:41.996][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:41.997][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:26:41.998][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:42.000][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:26:42.001][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:42.002][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:26:42.003][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:26:42.004][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:26:42.006][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:42.007][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-01 16:26:42.008][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:26:42.009][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:42.010][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:42.011][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:42.013][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:26:42.014][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:42.015][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:42.016][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:26:42.017][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:42.018][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:42.019][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:26:42.021][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:42.022][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:26:42.023][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:26:42.024][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:42.025][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:42.027][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:26:42.028][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.034][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[2025-03-01 16:26:42.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.121][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-01 16:26:42.122][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-01 16:26:42.124][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-01 16:26:42.126][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-01 16:26:42.127][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-01 16:26:42.129][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-01 16:26:42.130][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-01 16:26:42.132][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-01 16:26:42.133][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-01 16:26:42.135][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-01 16:26:42.136][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-01 16:26:42.138][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-01 16:26:42.139][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-01 16:26:42.141][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-01 16:26:42.143][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:26:42.144][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:26:42.146][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-01 16:26:42.147][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-01 16:26:42.149][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-01 16:26:42.150][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-01 16:26:42.152][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-01 16:26:42.153][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-01 16:26:42.155][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-01 16:26:42.156][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-01 16:26:42.158][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-01 16:26:42.159][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-01 16:26:42.161][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-01 16:26:42.163][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-01 16:26:42.164][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-01 16:26:42.166][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-01 16:26:42.167][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-01 16:26:42.169][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-01 16:26:42.170][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-01 16:26:42.172][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-01 16:26:42.173][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-01 16:26:42.175][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-01 16:26:42.176][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-01 16:26:42.178][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-01 16:26:42.179][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-01 16:26:42.181][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-01 16:26:42.182][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-01 16:26:42.184][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-01 16:26:42.185][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-01 16:26:42.187][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-01 16:26:42.188][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-01 16:26:42.190][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:26:42.191][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-01 16:26:42.193][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-01 16:26:42.194][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-01 16:26:42.196][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-01 16:26:42.197][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-01 16:26:42.199][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-01 16:26:42.200][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-01 16:26:42.202][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-01 16:26:42.203][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-01 16:26:42.205][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-01 16:26:42.206][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-01 16:26:42.208][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-01 16:26:42.209][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-01 16:26:42.211][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-01 16:26:42.213][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-01 16:26:42.214][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-01 16:26:42.216][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-01 16:26:42.217][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-01 16:26:42.219][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-01 16:26:42.220][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-01 16:26:42.222][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-01 16:26:42.223][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-01 16:26:42.225][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-01 16:26:42.226][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-01 16:26:42.228][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-01 16:26:42.229][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-01 16:26:42.231][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-01 16:26:42.232][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-01 16:26:42.234][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-01 16:26:42.235][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-01 16:26:42.237][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-01 16:26:42.238][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-01 16:26:42.240][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-01 16:26:42.241][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-01 16:26:42.243][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-01 16:26:42.244][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-01 16:26:42.246][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-01 16:26:42.248][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-01 16:26:42.250][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:26:42.251][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:26:42.252][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.254][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.255][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[2025-03-01 16:26:42.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.263][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[2025-03-01 16:26:42.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.306][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[2025-03-01 16:26:42.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.328][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[2025-03-01 16:26:42.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.343][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[2025-03-01 16:26:42.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.350][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[2025-03-01 16:26:42.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:26:42.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:42.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:42.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:42.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:42.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:42.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:26:42.750][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-03-01 16:26:44.197][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-03-01 16:26:44.200][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.201][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-03-01 16:26:44.203][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.204][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:26:44.206][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.207][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:26:44.208][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.209][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:26:44.210][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-03-01 16:26:44.211][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:26:44.213][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.214][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-03-01 16:26:44.215][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:26:44.216][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-03-01 16:26:44.216][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-03-01 16:26:44.217][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:44.218][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:44.220][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:26:44.221][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:44.222][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:44.223][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:26:44.224][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:44.225][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:44.226][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:26:44.227][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-03-01 16:26:44.227][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-03-01 16:26:44.228][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:26:44.229][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:26:44.231][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.232][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:44.233][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-03-01 16:26:44.235][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.236][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-03-01 16:26:44.237][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.238][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:26:44.240][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.241][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:26:44.242][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.243][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:26:44.244][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-01 16:26:44.245][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:26:44.247][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.248][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-03-01 16:26:44.249][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:26:44.250][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-03-01 16:26:44.250][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-03-01 16:26:44.250][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-03-01 16:26:44.250][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-03-01 16:26:44.250][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-03-01 16:26:44.250][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-03-01 16:26:44.251][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:44.252][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:26:44.254][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:26:44.255][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:44.256][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:44.257][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:26:44.258][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:44.259][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:44.260][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:26:44.261][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-03-01 16:26:44.261][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-03-01 16:26:44.262][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:26:44.263][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:26:44.264][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.266][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:44.267][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-03-01 16:26:44.269][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:44.270][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-03-01 16:26:44.271][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.272][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:26:44.274][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.275][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:26:44.276][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.277][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:26:44.278][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-01 16:26:44.279][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:26:44.280][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.282][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-03-01 16:26:44.283][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:26:44.284][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-03-01 16:26:44.284][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:26:44.284][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:26:44.284][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:26:44.284][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:26:44.284][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:26:44.284][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:26:44.284][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:26:44.284][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:26:44.284][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:26:44.284][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-03-01 16:26:44.284][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:26:44.284][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:26:44.284][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-03-01 16:26:44.285][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:44.286][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:26:44.286][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:26:44.286][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:26:44.288][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-03-01 16:26:44.289][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:44.290][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:44.291][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:26:44.292][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:44.293][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:44.294][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:26:44.295][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-03-01 16:26:44.295][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-03-01 16:26:44.295][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-03-01 16:26:44.296][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:26:44.297][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:26:44.299][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.300][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-03-01 16:26:44.301][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-03-01 16:26:44.303][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.304][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-03-01 16:26:44.305][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.307][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:26:44.308][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.309][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:26:44.310][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.311][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:26:44.312][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-01 16:26:44.313][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:26:44.315][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.316][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-03-01 16:26:44.317][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:26:44.318][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-03-01 16:26:44.318][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-03-01 16:26:44.319][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:26:44.320][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:26:44.321][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-03-01 16:26:44.323][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:44.324][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:44.325][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:26:44.326][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:26:44.327][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:26:44.328][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:26:44.329][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-03-01 16:26:44.329][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-03-01 16:26:44.329][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-03-01 16:26:44.330][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:26:44.331][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:26:44.332][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:26:44.334][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-03-01 16:26:44.335][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-03-01 16:26:44.337][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:26:44.338][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:26:44.340][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-03-01 16:26:44.342][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:26:44.343][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-03-01 16:26:44.349][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2025-03-01 16:26:44.350][super$initialize] Register connector ncbi.pubchem.subst with the request scheduler
biodb.DEBUG[2025-03-01 16:26:44.351][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.pubchem.subst.
biodb.DEBUG[2025-03-01 16:26:44.353][private$addConnectorRules] Create new rule for URL "pubchem.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.subst".
biodb.DEBUG[2025-03-01 16:26:44.354][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-03-01 16:26:44.355][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-03-01 16:26:44.357][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.subst".
biodb.DEBUG[2025-03-01 16:26:44.359][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-03-01 16:26:44.360][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2025-03-01 16:26:44.361][rule$addConnector] Connector "ncbi.pubchem.subst" is already listed in rule "pubchem.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-03-01 16:26:44.366][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2025-03-01 16:26:44.372][biodb::testThat]
biodb.INFO [2025-03-01 16:26:44.373][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-01 16:26:44.374][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:26:44.375][biodb::testThat]
biodb.TRACE[2025-03-01 16:26:44.762][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2025-03-01 16:26:44.764][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:26:44.768][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-03-01 16:26:44.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:26:44.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:44.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:44.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:44.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:44.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:44.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:26:44.785][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.786][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.789][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.795][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:44.796][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:44.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.798][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.800][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:44.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:44.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.804][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:44.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:44.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.809][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:44.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:44.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.818][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:44.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:44.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:26:44.851][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2025-03-01 16:26:44.854][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:26:44.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:26:44.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.859][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:26:44.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:26:44.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.863][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:26:44.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:26:44.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.868][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:26:44.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:26:44.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.873][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:26:44.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:26:44.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.877][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:26:44.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:26:44.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.882][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:26:44.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:26:44.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.898][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:44.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:44.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:44.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:44.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.938][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:44.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:44.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.943][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:44.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:44.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:44.947][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:44.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:44.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:44.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:45.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:45.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:45.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:45.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:45.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:45.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:45.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:45.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:45.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:45.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:45.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:45.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:45.345][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:45.347][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:45.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:45.349][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:45.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:45.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:45.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:45.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:45.364][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:45.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:45.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:45.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:45.369][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:45.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:45.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:45.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:45.374][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:45.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:45.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:45.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:45.385][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:45.386][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:45.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:45.389][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:45.390][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:45.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:45.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:45.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:45.403][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:45.404][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:45.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:45.407][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:45.413][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:45.414][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:45.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:45.416][ef$get] fields variable is a list.
biodb.INFO [2025-03-01 16:26:45.427][biodb::testThat]
biodb.INFO [2025-03-01 16:26:45.428][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-01 16:26:45.429][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:26:45.430][biodb::testThat]
biodb.DEBUG[2025-03-01 16:26:45.433][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-03-01 16:26:45.434][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-01 16:26:45.438][cch$loadFileContent] Trying to load 1 files from cache: [1]: "3".
biodb.TRACE[2025-03-01 16:26:45.440][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:26:47.545][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75/3.xml".
biodb.DEBUG[2025-03-01 16:26:47.547][conn$getEntryContent] 1 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:26:47.549][self$createEntryFromContent] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:26:47.550][self$createEntryFromContent] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-03-01 16:26:47.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:26:47.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:26:47.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:26:47.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:26:47.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:26:47.563][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:26:47.564][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.TRACE[2025-03-01 16:26:47.566][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:47.568][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:47.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.570][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:47.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:47.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.576][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:47.577][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:47.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.579][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.581][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:47.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-01 16:26:47.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.586][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:47.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:47.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.590][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:47.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:47.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:47.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:47.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.600][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:47.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-03-01 16:26:47.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:47.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:47.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:47.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:47.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:47.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:47.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:47.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:47.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:47.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:47.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:26:47.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:26:47.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:26:47.632][self$createEntryFromContent] Accession numbers: 3.
biodb.TRACE[2025-03-01 16:26:47.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-01 16:26:47.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-01 16:26:47.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:26:47.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:26:47.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:26:47.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:26:47.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-01 16:26:47.658][biodb::testThat]
biodb.INFO [2025-03-01 16:26:47.659][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-01 16:26:47.660][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:26:47.661][biodb::testThat]
biodb.INFO [2025-03-01 16:26:47.669][biodb::testThat]
biodb.INFO [2025-03-01 16:26:47.670][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-01 16:26:47.672][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:26:47.673][biodb::testThat]
biodb.WARN [2025-03-01 16:26:47.677][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-03-01 16:26:47.681][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-03-01 16:26:47.691][biodb::testThat]
biodb.INFO [2025-03-01 16:26:47.692][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-01 16:26:47.694][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:26:47.695][biodb::testThat]
biodb.TRACE[2025-03-01 16:26:47.706][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:26:47.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:26:47.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.711][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:26:47.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:26:47.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.716][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:26:47.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:26:47.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.721][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:26:47.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:26:47.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.725][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:26:47.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:26:47.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.730][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:26:47.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:26:47.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.734][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:26:47.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:26:47.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.740][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:26:47.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:26:47.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.745][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-03-01 16:26:47.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-03-01 16:26:47.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.750][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:26:47.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-03-01 16:26:47.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.754][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:26:47.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:26:47.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.759][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:26:47.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:26:47.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.764][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:26:47.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:26:47.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:26:47.768][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:26:47.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:26:47.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:26:47.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-01 16:26:47.780][biodb::testThat]
biodb.INFO [2025-03-01 16:26:47.781][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-01 16:26:47.782][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:26:47.783][biodb::testThat]
biodb.INFO [2025-03-01 16:26:47.794][biodb::testThat]
biodb.INFO [2025-03-01 16:26:47.795][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-01 16:26:47.796][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:26:47.797][biodb::testThat]
biodb.INFO [2025-03-01 16:26:47.807][biodb::testThat]
biodb.INFO [2025-03-01 16:26:47.808][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-01 16:26:47.809][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:26:47.811][biodb::testThat]
biodb.DEBUG[2025-03-01 16:26:47.815][function(conn, opt)] Trying to download "https://pubchem.ncbi.nlm.nih.gov/substance/3".
biodb.DEBUG[2025-03-01 16:26:58.857][getUrlContent] Use base::url() for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/substance/3.
biodb.INFO [2025-03-01 16:27:09.957][biodb::testThat]
biodb.INFO [2025-03-01 16:27:09.958][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-01 16:27:09.960][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:27:09.961][biodb::testThat]
biodb.DEBUG[2025-03-01 16:27:21.006][getUrlContent] Use base::url() for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?sid=3&t=l.
biodb.INFO [2025-03-01 16:27:32.074][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-01 16:27:32.076][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.pubchem.subst from the request scheduler
biodb.INFO [2025-03-01 16:27:32.077][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2025-03-01 16:27:32.079][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-01 16:27:32.080][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:27:32.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:27:32.082][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:27:32.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:27:32.084][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:27:32.085][FUN] Functions in observer 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 39 | WARN 1 | SKIP 0 | PASS 702 ]

══ 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_100_ccds.R:37:1'): The entry page URL can be downloaded. ──
!is.na(content) is not TRUE

`actual`:       
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.na(content))
── Failure ('test_long_100_ccds.R:37:1'): The entry page URL can be downloaded. ──
nchar(content) > 0 is not TRUE

`actual`:       
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(nchar(content) > 0)
── 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")
── Failure ('test_long_200_gene.R:37:1'): The entry page URL can be downloaded. ──
!is.na(content) is not TRUE

`actual`:       
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.na(content))
── Failure ('test_long_200_gene.R:37:1'): The entry page URL can be downloaded. ──
nchar(content) > 0 is not TRUE

`actual`:       
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(nchar(content) > 0)
── Failure ('test_long_300_pubchem.comp.R:37:1'): The entry page URL can be downloaded. ──
!is.na(content) is not TRUE

`actual`:       
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.na(content))
── Failure ('test_long_300_pubchem.comp.R:37:1'): The entry page URL can be downloaded. ──
nchar(content) > 0 is not TRUE

`actual`:       
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(nchar(content) > 0)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry image URL can be downloaded. ──
Error in `charToRaw(content)`: argument must be a character vector of length 1
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─biodb:::getUrlContent(url, binary = TRUE)
 4.     └─biodb:::getBaseUrlContent(u, binary = binary)
 5.       └─base::charToRaw(content)
── 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)
── Failure ('test_long_400_pubchem.subst.R:37:1'): The entry page URL can be downloaded. ──
!is.na(content) is not TRUE

`actual`:       
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.na(content))
── Failure ('test_long_400_pubchem.subst.R:37:1'): The entry page URL can be downloaded. ──
nchar(content) > 0 is not TRUE

`actual`:       
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(nchar(content) > 0)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry image URL can be downloaded. ──
Error in `charToRaw(content)`: argument must be a character vector of length 1
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─biodb:::getUrlContent(url, binary = TRUE)
 4.     └─biodb:::getBaseUrlContent(u, binary = binary)
 5.       └─base::charToRaw(content)

[ FAIL 39 | WARN 1 | SKIP 0 | PASS 702 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '1.10.0'
* 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 ... NOTE
  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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... WARNING
'library' or 'require' call not declared from: 'biodbNci'
* checking tests in 'longtests' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
   2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
   3.   └─testthat::expect_true(nchar(content) > 0)
  ── Error ('test_long_400_pubchem.subst.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 39 | WARN 1 | SKIP 0 | PASS 702 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNcbi.Rcheck/00check.log'
for details.

Installation output

biodbNcbi.Rcheck/00install.out

* installing *source* package 'biodbNcbi' ...
** 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)