Back to Long Tests report for BioC 3.19

This page was generated on 2024-05-04 23:55:02 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
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 11/33HostnameOS / ArchCHECK
biodbNcbi 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-04 09:55:02 -0400 (Sat, 04 May 2024)
git_url: https://git.bioconductor.org/packages/biodbNcbi
git_branch: RELEASE_3_19
git_last_commit: 1365c98
git_last_commit_date: 2024-04-30 11:41:09 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino3Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  WARNINGS  

CHECK results for biodbNcbi on palomino3


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: 1.8.0
Command: F:\biocbuild\bbs-3.19-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_1.8.0.tar.gz
StartedAt: 2024-05-04 16:06:41 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 16:08:06 -0400 (Sat, 04 May 2024)
EllapsedTime: 84.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNcbi.Rcheck
Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

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

Type 'demo()' for some demos, 'help()' for on-line help, or
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNcbi")
Loading required package: biodbNcbi
biodb.INFO [2024-05-04 16:07:29.635][biodb::testContext]
biodb.INFO [2024-05-04 16:07:29.638][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:07:29.639][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2024-05-04 16:07:29.641][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:07:29.642][biodb::testContext]
biodb.INFO [2024-05-04 16:07:29.648][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:07:29.651][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-04 16:07:29.658][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:07:29.659][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-04 16:07:29.661][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-04 16:07:29.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.665][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-04 16:07:29.681][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-04 16:07:29.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.686][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-04 16:07:29.687][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-04 16:07:29.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.691][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-04 16:07:29.692][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-04 16:07:29.694][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-04 16:07:29.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.697][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[2024-05-04 16:07:29.698][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-04 16:07:29.699][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-04 16:07:29.700][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-04 16:07:29.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.705][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-04 16:07:29.706][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-04 16:07:29.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.710][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-04 16:07:29.712][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-04 16:07:29.713][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-04 16:07:29.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.717][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-04 16:07:29.718][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-04 16:07:29.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.723][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-04 16:07:29.724][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-04 16:07:29.725][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-04 16:07:29.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.730][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:07:29.731][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-04 16:07:29.732][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-04 16:07:29.733][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-04 16:07:29.734][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-04 16:07:29.736][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-04 16:07:29.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.740][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-04 16:07:29.741][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-04 16:07:29.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.746][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-04 16:07:29.747][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-04 16:07:29.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.751][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-04 16:07:29.753][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-04 16:07:29.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.757][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-04 16:07:29.758][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-04 16:07:29.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.763][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-04 16:07:29.764][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-04 16:07:29.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.768][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:07:29.770][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-04 16:07:29.773][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-04 16:07:29.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.778][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-04 16:07:29.779][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-04 16:07:29.780][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-04 16:07:29.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.787][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-04 16:07:29.822][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:29.836][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-04 16:07:29.838][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.839][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:29.840][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.841][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:29.842][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:29.844][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:29.845][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:07:29.846][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:29.847][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.848][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-04 16:07:29.850][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:29.851][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:29.852][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.853][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:07:29.853][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:07:29.853][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:07:29.853][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:07:29.853][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:07:29.854][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:29.855][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:29.857][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:29.858][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:29.859][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:29.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:29.861][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:29.862][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:29.864][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:29.866][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:29.867][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:29.868][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:29.870][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-04 16:07:29.872][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:29.873][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:07:29.874][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.875][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:29.876][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.878][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:29.879][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:29.880][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:29.881][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:07:29.882][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:29.884][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.885][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-04 16:07:29.886][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:29.887][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:29.888][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.890][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:07:29.890][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:07:29.890][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:07:29.890][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:07:29.890][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:07:29.891][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:29.892][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:29.893][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:29.894][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:29.895][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:29.896][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:29.898][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:29.899][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:29.900][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:29.901][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:29.902][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:29.903][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:29.905][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-04 16:07:29.907][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.908][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-04 16:07:29.909][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.910][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:29.911][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.913][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:29.914][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:29.915][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:29.916][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:07:29.917][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:29.919][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:29.920][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-04 16:07:29.921][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:29.922][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:29.923][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.925][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:29.926][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:29.927][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:29.928][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:29.929][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:29.930][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:29.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:29.933][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:29.934][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:29.935][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:29.936][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:29.937][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:29.938][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:29.940][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-04 16:07:29.942][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.943][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:07:29.944][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.945][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:29.947][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.948][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:29.949][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:29.950][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:29.951][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:07:29.953][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:29.954][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:29.955][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-04 16:07:29.956][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:29.957][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:29.959][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:29.960][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:29.961][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:29.962][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:29.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:29.964][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:29.966][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:29.967][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:29.968][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:29.969][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:29.970][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:29.971][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:29.972][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:29.974][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:29.977][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:07:29.978][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:29.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:29.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:29.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:29.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:29.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:29.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:29.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:29.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:29.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:29.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.029][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[2024-05-04 16:07:30.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.034][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[2024-05-04 16:07:30.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.045][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[2024-05-04 16:07:30.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.050][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[2024-05-04 16:07:30.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.061][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[2024-05-04 16:07:30.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.079][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-04 16:07:30.083][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-04 16:07:30.085][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-04 16:07:30.086][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-04 16:07:30.088][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 16:07:30.089][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-04 16:07:30.091][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-04 16:07:30.093][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-04 16:07:30.094][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 16:07:30.096][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-04 16:07:30.097][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 16:07:30.099][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-04 16:07:30.100][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-04 16:07:30.102][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-04 16:07:30.103][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 16:07:30.105][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 16:07:30.106][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-04 16:07:30.108][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-04 16:07:30.110][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 16:07:30.111][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-04 16:07:30.113][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-04 16:07:30.114][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-04 16:07:30.116][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-04 16:07:30.117][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-04 16:07:30.119][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-04 16:07:30.120][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-04 16:07:30.122][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-04 16:07:30.123][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-04 16:07:30.125][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-04 16:07:30.127][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-04 16:07:30.128][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-04 16:07:30.130][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-04 16:07:30.131][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-04 16:07:30.133][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-04 16:07:30.134][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-04 16:07:30.136][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-04 16:07:30.137][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-04 16:07:30.139][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-04 16:07:30.140][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-04 16:07:30.142][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-04 16:07:30.144][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-04 16:07:30.145][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-04 16:07:30.147][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-04 16:07:30.148][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-04 16:07:30.150][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-04 16:07:30.151][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 16:07:30.153][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-04 16:07:30.154][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-04 16:07:30.156][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-04 16:07:30.158][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-04 16:07:30.159][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-04 16:07:30.161][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-04 16:07:30.162][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-04 16:07:30.164][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-04 16:07:30.165][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-04 16:07:30.167][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-04 16:07:30.168][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-04 16:07:30.170][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-04 16:07:30.171][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-04 16:07:30.173][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-04 16:07:30.175][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-04 16:07:30.176][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-04 16:07:30.178][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-04 16:07:30.179][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-04 16:07:30.181][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-04 16:07:30.182][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-04 16:07:30.184][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 16:07:30.185][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 16:07:30.187][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-04 16:07:30.189][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-04 16:07:30.190][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-04 16:07:30.192][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-04 16:07:30.193][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-04 16:07:30.195][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-04 16:07:30.196][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-04 16:07:30.198][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-04 16:07:30.199][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-04 16:07:30.201][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-04 16:07:30.203][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-04 16:07:30.204][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-04 16:07:30.206][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-04 16:07:30.207][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-04 16:07:30.209][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-04 16:07:30.251][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-04 16:07:30.254][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:07:30.257][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:07:30.259][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.263][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.284][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[2024-05-04 16:07:30.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.292][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[2024-05-04 16:07:30.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.300][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[2024-05-04 16:07:30.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.372][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[2024-05-04 16:07:30.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:30.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:30.407][bdb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2024-05-04 16:07:30.417][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2024-05-04 16:07:30.420][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.421][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2024-05-04 16:07:30.423][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.424][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:30.425][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.426][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:30.428][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.429][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:30.430][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2024-05-04 16:07:30.431][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:30.433][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.434][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2024-05-04 16:07:30.435][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:30.436][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2024-05-04 16:07:30.436][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2024-05-04 16:07:30.437][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:30.439][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:30.440][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 16:07:30.441][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:30.442][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:30.444][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:30.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:30.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:30.447][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:30.449][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2024-05-04 16:07:30.449][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2024-05-04 16:07:30.450][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:30.451][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:30.452][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.453][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:30.455][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2024-05-04 16:07:30.457][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.458][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2024-05-04 16:07:30.460][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.461][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:30.491][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.492][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:30.494][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.495][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:30.496][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 16:07:30.497][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:30.499][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.500][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2024-05-04 16:07:30.501][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:30.502][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2024-05-04 16:07:30.502][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2024-05-04 16:07:30.502][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2024-05-04 16:07:30.502][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2024-05-04 16:07:30.502][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2024-05-04 16:07:30.502][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2024-05-04 16:07:30.504][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:30.505][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:07:30.506][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 16:07:30.507][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:30.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:30.510][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:30.511][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:30.513][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:30.514][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:30.515][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2024-05-04 16:07:30.515][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2024-05-04 16:07:30.516][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:30.517][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:30.518][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.520][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:30.521][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2024-05-04 16:07:30.523][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:30.525][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2024-05-04 16:07:30.526][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.528][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:30.529][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.531][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:30.532][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.533][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:30.534][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 16:07:30.536][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:30.537][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.538][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2024-05-04 16:07:30.539][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:30.541][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2024-05-04 16:07:30.541][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:30.541][self$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[2024-05-04 16:07:30.541][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:30.541][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:30.541][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:30.541][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:30.541][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:30.541][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:30.541][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:30.541][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2024-05-04 16:07:30.541][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:30.541][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:30.541][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:30.542][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:30.544][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:07:30.544][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:07:30.544][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:07:30.545][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2024-05-04 16:07:30.546][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:30.547][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:30.548][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:30.549][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:30.551][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:30.552][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:30.553][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2024-05-04 16:07:30.553][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2024-05-04 16:07:30.553][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2024-05-04 16:07:30.554][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:30.555][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:30.557][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.558][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2024-05-04 16:07:30.560][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2024-05-04 16:07:30.562][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.563][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2024-05-04 16:07:30.564][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.566][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:30.567][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.568][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:30.569][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.571][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:30.572][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 16:07:30.574][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:30.575][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.576][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2024-05-04 16:07:30.577][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:30.578][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2024-05-04 16:07:30.578][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2024-05-04 16:07:30.580][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:30.581][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:30.583][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2024-05-04 16:07:30.584][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:30.586][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:30.588][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:30.590][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:30.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:30.595][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:30.597][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2024-05-04 16:07:30.597][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2024-05-04 16:07:30.597][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2024-05-04 16:07:30.600][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:30.602][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:30.604][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:30.606][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2024-05-04 16:07:30.617][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2024-05-04 16:07:30.620][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 16:07:30.623][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 16:07:30.626][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2024-05-04 16:07:30.628][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 16:07:30.631][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2024-05-04 16:07:30.651][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2024-05-04 16:07:30.653][initialize] Register connector ncbi.ccds with the request scheduler
biodb.DEBUG[2024-05-04 16:07:30.657][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.ccds.
biodb.DEBUG[2024-05-04 16:07:30.661][private$addConnectorRules] Create new rule for URL "www.ncbi.nlm.nih.gov" of connector "ncbi.ccds".
biodb.DEBUG[2024-05-04 16:07:30.664][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:30.665][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:30.667][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.ccds".
biodb.DEBUG[2024-05-04 16:07:30.669][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:30.670][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:30.671][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2024-05-04 16:07:30.681][biodb::testThat]
biodb.INFO [2024-05-04 16:07:30.683][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-04 16:07:30.684][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:30.686][biodb::testThat]
biodb.TRACE[2024-05-04 16:07:30.693][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2024-05-04 16:07:30.695][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2024-05-04 16:07:30.698][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2024-05-04 16:07:30.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:30.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:30.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:30.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:30.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:30.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:30.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:30.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:30.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:30.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.770][ef$get] Asked field names are: sequence.
biodb.TRACE[2024-05-04 16:07:30.781][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:30.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.784][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.807][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2024-05-04 16:07:30.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:30.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.812][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:30.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:30.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.817][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:30.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:30.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:30.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:30.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.827][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:30.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:30.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:30.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:30.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:30.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:30.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:30.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:30.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:30.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:30.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:30.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:30.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:30.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:30.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:30.923][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2024-05-04 16:07:30.927][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:30.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:30.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.932][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:30.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:30.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.967][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:30.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:30.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.975][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:30.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:30.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.983][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:30.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:30.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:30.993][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:30.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:30.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:30.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.042][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.085][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.090][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.095][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.130][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.132][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.134][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.150][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2024-05-04 16:07:31.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.155][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.160][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.165][ef$get] Asked field names are: sequence.
biodb.TRACE[2024-05-04 16:07:31.166][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.168][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.169][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2024-05-04 16:07:31.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.184][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.186][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.188][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.195][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.196][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.198][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.218][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2024-05-04 16:07:31.248][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2024-05-04 16:07:31.250][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2024-05-04 16:07:31.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:31.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:31.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:31.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:31.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:31.268][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:31.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:31.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.299][ef$get] Asked field names are: sequence.
biodb.TRACE[2024-05-04 16:07:31.301][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.303][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.305][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2024-05-04 16:07:31.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.310][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.314][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.324][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:31.358][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2024-05-04 16:07:31.376][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.381][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.386][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:31.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:31.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.391][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:31.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:31.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.396][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:31.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:31.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.401][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:31.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:31.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.423][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.464][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.469][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.474][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:31.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.512][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.513][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.515][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.531][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2024-05-04 16:07:31.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.536][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.541][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.546][ef$get] Asked field names are: sequence.
biodb.TRACE[2024-05-04 16:07:31.547][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.549][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.551][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2024-05-04 16:07:31.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.565][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.567][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:31.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.569][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:31.576][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:31.577][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:31.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:31.579][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 16:07:31.592][biodb::testThat]
biodb.INFO [2024-05-04 16:07:31.593][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-04 16:07:31.594][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:31.596][biodb::testThat]
biodb.DEBUG[2024-05-04 16:07:31.598][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2024-05-04 16:07:31.610][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-04 16:07:31.616][cch$loadFileContent] Trying to load 2 files from cache: [2]: "CCDS12227.1, CCDS43240.1".
biodb.INFO [2024-05-04 16:07:31.617][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704" for "ncbi.ccds-c3bf0257a03be04fd46e362b99907704".
biodb.TRACE[2024-05-04 16:07:31.619][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-05-04 16:07:31.621][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 16:07:31.622][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 16:07:31.623][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2024-05-04 16:07:31.625][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 16:07:31.626][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 16:07:31.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:31.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:31.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:31.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:31.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:31.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:31.644][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[2024-05-04 16:07:31.646][scheduler$sendRequest] Getting content of get URL request "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.DEBUG[2024-05-04 16:07:31.664][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 16:07:31.665][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 16:07:31.667][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.TRACE[2024-05-04 16:07:32.954][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1).
biodb.DEBUG[2024-05-04 16:07:34.311][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 16:07:34.314][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/91a3a15871253de20fe3aa9cc158f120.content"
biodb.TRACE[2024-05-04 16:07:34.329][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/91a3a15871253de20fe3aa9cc158f120.request"
biodb.INFO [2024-05-04 16:07:34.369][biodb::testThat]
biodb.INFO [2024-05-04 16:07:34.370][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-04 16:07:34.371][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:34.373][biodb::testThat]
biodb.INFO [2024-05-04 16:07:34.382][biodb::testThat]
biodb.INFO [2024-05-04 16:07:34.384][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-04 16:07:34.385][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:34.386][biodb::testThat]
biodb.WARN [2024-05-04 16:07:34.413][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-05-04 16:07:34.432][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-05-04 16:07:34.449][biodb::testThat]
biodb.INFO [2024-05-04 16:07:34.450][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-04 16:07:34.451][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:34.453][biodb::testThat]
biodb.DEBUG[2024-05-04 16:07:34.471][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2024-05-04 16:07:34.519][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 16:07:34.534][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS12227.1".
biodb.TRACE[2024-05-04 16:07:34.536][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 16:07:34.537][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 16:07:34.538][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 16:07:34.540][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2024-05-04 16:07:34.541][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 16:07:34.542][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 16:07:34.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:34.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:34.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:34.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:34.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:34.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:34.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:34.592][scheduler$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[2024-05-04 16:07:34.596][scheduler$sendRequest] Loading content of request from cache.
biodb.TRACE[2024-05-04 16:07:34.597][cch$loadFileContent] Trying to load 1 files from cache: [1]: "91a3a15871253de20fe3aa9cc158f120".
biodb.TRACE[2024-05-04 16:07:34.599][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 16:07:34.694][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/91a3a15871253de20fe3aa9cc158f120.content".
biodb.TRACE[2024-05-04 16:07:34.698][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/CCDS12227.1.html"
biodb.INFO [2024-05-04 16:07:34.741][biodb::testThat]
biodb.INFO [2024-05-04 16:07:34.742][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-04 16:07:34.744][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:34.745][biodb::testThat]
biodb.INFO [2024-05-04 16:07:34.757][biodb::testThat]
biodb.INFO [2024-05-04 16:07:34.759][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-04 16:07:34.760][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:34.761][biodb::testThat]
biodb.INFO [2024-05-04 16:07:34.772][biodb::testThat]
biodb.INFO [2024-05-04 16:07:34.773][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-04 16:07:34.775][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:34.776][biodb::testThat]
biodb.DEBUG[2024-05-04 16:07:34.781][function(conn, opt)] Trying to download "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1".
biodb.DEBUG[2024-05-04 16:07:36.115][getUrlContent] Use RCurl for downloading content of URL https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS12227.1.
biodb.INFO [2024-05-04 16:07:37.511][biodb::testThat]
biodb.INFO [2024-05-04 16:07:37.512][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-04 16:07:37.514][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:37.515][biodb::testThat]
biodb.INFO [2024-05-04 16:07:37.524][bdb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-04 16:07:37.530][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.ccds from the request scheduler
biodb.INFO [2024-05-04 16:07:37.533][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2024-05-04 16:07:37.534][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-04 16:07:37.535][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:37.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:37.538][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.540][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.541][FUN] Functions in observer BiodbConfig: [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 [2024-05-04 16:07:37.551][biodb::testContext]
biodb.INFO [2024-05-04 16:07:37.553][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:07:37.554][biodb::testContext] Test context - Gene long tests
biodb.INFO [2024-05-04 16:07:37.555][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:07:37.556][biodb::testContext]
biodb.INFO [2024-05-04 16:07:37.559][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:07:37.561][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-04 16:07:37.567][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:07:37.568][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-04 16:07:37.569][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-04 16:07:37.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.574][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-04 16:07:37.575][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-04 16:07:37.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.580][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-04 16:07:37.581][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-04 16:07:37.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.585][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-04 16:07:37.586][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-04 16:07:37.588][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-04 16:07:37.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.592][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-04 16:07:37.593][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-04 16:07:37.595][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-04 16:07:37.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.599][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-04 16:07:37.600][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-04 16:07:37.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.605][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-04 16:07:37.606][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-04 16:07:37.607][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-04 16:07:37.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.612][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-04 16:07:37.613][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-04 16:07:37.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.618][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-04 16:07:37.619][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-04 16:07:37.620][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-04 16:07:37.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.625][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:07:37.626][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-04 16:07:37.627][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-04 16:07:37.628][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-04 16:07:37.630][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-04 16:07:37.631][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-04 16:07:37.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.635][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-04 16:07:37.637][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-04 16:07:37.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.641][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-04 16:07:37.642][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-04 16:07:37.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.647][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-04 16:07:37.648][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-04 16:07:37.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.653][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-04 16:07:37.654][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-04 16:07:37.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.664][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-04 16:07:37.665][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-04 16:07:37.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.670][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:07:37.671][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-04 16:07:37.675][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-04 16:07:37.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.679][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-04 16:07:37.680][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-04 16:07:37.681][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-04 16:07:37.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.686][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-04 16:07:37.688][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:37.689][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-04 16:07:37.691][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.692][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:37.693][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.694][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:37.695][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:37.697][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:37.698][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:07:37.699][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:37.700][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.701][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-04 16:07:37.703][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:37.704][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:37.705][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.706][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:07:37.706][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:07:37.706][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:07:37.706][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:07:37.706][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:07:37.707][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:37.709][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:37.710][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:37.711][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:37.712][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:37.713][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:37.714][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:37.715][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:37.717][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:37.718][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:37.719][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:37.720][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:37.721][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-04 16:07:37.723][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:37.725][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:07:37.726][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.727][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:37.728][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.730][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:37.731][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:37.732][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:37.733][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:07:37.734][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:37.736][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.737][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-04 16:07:37.738][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:37.739][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:37.740][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.742][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:07:37.742][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:07:37.742][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:07:37.742][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:07:37.742][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:07:37.743][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:37.744][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:37.745][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:37.746][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:37.748][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:37.749][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:37.750][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:37.751][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:37.752][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:37.753][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:37.754][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:37.756][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:37.757][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-04 16:07:37.759][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.760][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-04 16:07:37.761][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.763][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:37.764][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.765][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:37.766][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:37.767][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:37.769][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:07:37.770][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:37.771][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:37.772][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-04 16:07:37.774][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:37.775][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:37.776][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.777][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:37.778][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:37.780][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:37.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:37.782][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:37.783][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:37.789][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:37.790][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:37.792][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:37.793][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:37.794][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:37.795][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:37.796][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:37.798][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-04 16:07:37.800][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.801][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:07:37.802][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.803][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:37.805][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.806][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:37.807][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:37.808][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:37.810][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:07:37.811][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:37.812][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:37.813][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-04 16:07:37.815][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:37.816][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:37.817][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:37.818][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:37.820][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:37.821][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:37.822][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:37.823][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:37.824][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:37.825][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:37.827][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:37.828][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:37.829][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:37.830][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:37.831][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:37.832][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:37.834][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:07:37.835][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.858][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[2024-05-04 16:07:37.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.907][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[2024-05-04 16:07:37.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:37.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:37.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:37.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:37.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:37.935][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-04 16:07:37.937][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-04 16:07:37.939][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-04 16:07:37.940][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-04 16:07:37.942][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 16:07:37.943][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-04 16:07:37.945][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-04 16:07:37.947][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-04 16:07:37.949][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 16:07:37.951][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-04 16:07:37.952][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 16:07:37.954][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-04 16:07:37.955][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-04 16:07:37.957][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-04 16:07:37.959][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 16:07:37.960][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 16:07:37.962][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-04 16:07:37.963][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-04 16:07:37.965][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 16:07:37.966][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-04 16:07:37.968][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-04 16:07:37.969][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-04 16:07:37.971][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-04 16:07:37.973][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-04 16:07:37.974][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-04 16:07:37.976][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-04 16:07:37.977][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-04 16:07:37.979][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-04 16:07:37.981][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-04 16:07:37.982][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-04 16:07:37.984][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-04 16:07:37.985][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-04 16:07:37.987][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-04 16:07:37.988][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-04 16:07:37.990][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-04 16:07:37.991][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-04 16:07:37.993][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-04 16:07:37.995][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-04 16:07:37.996][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-04 16:07:37.998][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-04 16:07:37.999][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-04 16:07:38.001][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-04 16:07:38.003][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-04 16:07:38.004][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-04 16:07:38.006][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-04 16:07:38.007][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 16:07:38.009][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-04 16:07:38.011][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-04 16:07:38.012][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-04 16:07:38.014][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-04 16:07:38.015][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-04 16:07:38.017][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-04 16:07:38.019][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-04 16:07:38.020][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-04 16:07:38.022][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-04 16:07:38.023][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-04 16:07:38.025][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-04 16:07:38.032][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-04 16:07:38.034][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-04 16:07:38.035][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-04 16:07:38.037][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-04 16:07:38.038][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-04 16:07:38.040][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-04 16:07:38.041][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-04 16:07:38.043][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-04 16:07:38.045][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-04 16:07:38.046][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 16:07:38.048][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 16:07:38.049][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-04 16:07:38.051][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-04 16:07:38.052][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-04 16:07:38.054][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-04 16:07:38.056][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-04 16:07:38.057][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-04 16:07:38.059][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-04 16:07:38.060][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-04 16:07:38.062][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-04 16:07:38.064][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-04 16:07:38.065][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-04 16:07:38.067][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-04 16:07:38.068][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-04 16:07:38.070][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-04 16:07:38.071][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-04 16:07:38.073][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-04 16:07:38.075][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:07:38.077][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:07:38.078][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.080][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:38.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:38.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:38.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:38.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:38.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:38.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:38.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:38.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:38.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.157][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[2024-05-04 16:07:38.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:38.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.172][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[2024-05-04 16:07:38.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.180][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[2024-05-04 16:07:38.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.187][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[2024-05-04 16:07:38.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.195][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[2024-05-04 16:07:38.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:38.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.210][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[2024-05-04 16:07:38.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:38.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.218][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[2024-05-04 16:07:38.221][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2024-05-04 16:07:38.223][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2024-05-04 16:07:38.225][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.227][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2024-05-04 16:07:38.228][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.229][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:38.230][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.232][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:38.233][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.234][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:38.235][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2024-05-04 16:07:38.236][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:38.238][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.239][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2024-05-04 16:07:38.240][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:38.241][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2024-05-04 16:07:38.241][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2024-05-04 16:07:38.243][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:38.244][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:38.245][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 16:07:38.246][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:38.247][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:38.248][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:38.250][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:38.251][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:38.252][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:38.253][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2024-05-04 16:07:38.253][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2024-05-04 16:07:38.254][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:38.255][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:38.257][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.258][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:38.259][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2024-05-04 16:07:38.261][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.262][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2024-05-04 16:07:38.264][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.265][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:38.266][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.267][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:38.269][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.270][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:38.271][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 16:07:38.272][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:38.279][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.280][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2024-05-04 16:07:38.281][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:38.282][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2024-05-04 16:07:38.282][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2024-05-04 16:07:38.282][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2024-05-04 16:07:38.282][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2024-05-04 16:07:38.282][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2024-05-04 16:07:38.282][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2024-05-04 16:07:38.284][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:38.285][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:07:38.286][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 16:07:38.287][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:38.288][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:38.290][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:38.291][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:38.292][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:38.293][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:38.294][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2024-05-04 16:07:38.294][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2024-05-04 16:07:38.295][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:38.297][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:38.298][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.299][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:38.300][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2024-05-04 16:07:38.303][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:38.304][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2024-05-04 16:07:38.305][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.306][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:38.308][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.309][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:38.310][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.311][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:38.312][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 16:07:38.314][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:38.315][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.316][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2024-05-04 16:07:38.317][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:38.318][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2024-05-04 16:07:38.318][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:38.318][self$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[2024-05-04 16:07:38.318][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:38.318][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:38.318][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:38.318][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:38.318][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:38.318][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:38.318][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:38.318][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2024-05-04 16:07:38.318][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:38.318][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:38.318][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:38.320][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:38.321][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:07:38.321][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:07:38.321][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:07:38.322][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2024-05-04 16:07:38.324][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:38.325][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:38.326][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:38.327][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:38.328][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:38.329][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:38.330][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2024-05-04 16:07:38.330][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2024-05-04 16:07:38.330][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2024-05-04 16:07:38.332][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:38.333][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:38.334][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.335][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2024-05-04 16:07:38.337][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2024-05-04 16:07:38.339][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.340][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2024-05-04 16:07:38.341][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.342][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:38.344][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.345][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:38.346][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.347][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:38.348][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 16:07:38.350][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:38.351][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.352][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2024-05-04 16:07:38.353][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:38.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2024-05-04 16:07:38.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2024-05-04 16:07:38.356][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:38.357][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:38.358][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2024-05-04 16:07:38.359][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:38.360][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:38.361][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:38.363][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:38.364][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:38.365][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:38.366][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2024-05-04 16:07:38.366][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2024-05-04 16:07:38.366][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2024-05-04 16:07:38.367][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:38.368][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:38.370][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:38.371][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2024-05-04 16:07:38.372][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2024-05-04 16:07:38.374][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 16:07:38.376][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 16:07:38.378][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2024-05-04 16:07:38.379][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 16:07:38.381][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2024-05-04 16:07:38.388][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2024-05-04 16:07:38.389][super$initialize] Register connector ncbi.gene with the request scheduler
biodb.DEBUG[2024-05-04 16:07:38.391][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.gene.
biodb.DEBUG[2024-05-04 16:07:38.393][private$addConnectorRules] Create new rule for URL "www.ncbi.nlm.nih.gov" of connector "ncbi.gene".
biodb.DEBUG[2024-05-04 16:07:38.400][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:38.401][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:38.403][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.gene".
biodb.DEBUG[2024-05-04 16:07:38.404][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:38.406][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:38.463][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2024-05-04 16:07:38.469][biodb::testThat]
biodb.INFO [2024-05-04 16:07:38.470][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-04 16:07:38.471][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:38.472][biodb::testThat]
biodb.TRACE[2024-05-04 16:07:38.484][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2024-05-04 16:07:38.486][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2024-05-04 16:07:38.489][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2024-05-04 16:07:38.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:38.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:38.524][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:38.526][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:38.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.528][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:38.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:38.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.536][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-04 16:07:38.537][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-04 16:07:38.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.539][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.542][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-04 16:07:38.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-04 16:07:38.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.547][ef$get] Asked field names are: location.
biodb.TRACE[2024-05-04 16:07:38.548][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2024-05-04 16:07:38.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.550][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.552][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2024-05-04 16:07:38.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2024-05-04 16:07:38.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.558][ef$get] Asked field names are: symbol.
biodb.TRACE[2024-05-04 16:07:38.559][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2024-05-04 16:07:38.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.561][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.563][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2024-05-04 16:07:38.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2024-05-04 16:07:38.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.568][ef$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-04 16:07:38.570][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:38.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.572][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.574][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-04 16:07:38.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:38.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.579][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2024-05-04 16:07:38.581][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2024-05-04 16:07:38.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.583][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.587][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2024-05-04 16:07:38.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2024-05-04 16:07:38.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.596][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:38.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:38.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.601][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2024-05-04 16:07:38.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2024-05-04 16:07:38.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.606][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2024-05-04 16:07:38.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2024-05-04 16:07:38.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:38.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:38.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.616][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2024-05-04 16:07:38.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2024-05-04 16:07:38.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:38.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:38.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:38.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:38.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:38.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:38.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:38.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:38.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:38.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:38.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:38.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:38.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:38.688][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2024-05-04 16:07:38.691][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:38.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:38.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.696][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:38.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:38.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.701][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:38.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:38.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.706][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:38.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:38.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:38.711][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:38.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:38.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:38.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:38.716][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2024-05-04 16:07:38.743][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2024-05-04 16:07:38.744][initialize] Register connector ncbi.ccds with the request scheduler
biodb.DEBUG[2024-05-04 16:07:38.746][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.ccds.
biodb.DEBUG[2024-05-04 16:07:38.917][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2024-05-04 16:07:38.918][self$recomputeFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:38.919][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2024-05-04 16:07:38.930][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:38.932][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:38.933][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2024-05-04 16:07:38.935][self$recomputeFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:38.936][self$recomputeFrequency] t.conn=1.000000, n.conn=3.000000
biodb.DEBUG[2024-05-04 16:07:38.937][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:38.938][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:38.954][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2024-05-04 16:07:38.956][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2024-05-04 16:07:38.959][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 16:07:38.964][cch$loadFileContent] Trying to load 1 files from cache: [1]: "CCDS14416.1".
biodb.TRACE[2024-05-04 16:07:38.966][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 16:07:38.967][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 16:07:38.969][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 16:07:38.970][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2024-05-04 16:07:38.971][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 16:07:38.973][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 16:07:38.976][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:38.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:38.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:38.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:38.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:38.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:38.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:38.990][scheduler$sendRequest] Getting content of get URL request "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.DEBUG[2024-05-04 16:07:38.993][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 16:07:38.994][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 16:07:38.996][private$doSendRequestOnce] Sent URL is "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1".
biodb.TRACE[2024-05-04 16:07:40.264][getRCurlRequestResult] Using RCurl package for sending request (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=CCDS14416.1).
biodb.DEBUG[2024-05-04 16:07:41.970][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 16:07:41.973][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704/cb67b3a5b745c7932ff9adec9d1972cf.content"
biodb.INFO [2024-05-04 16:07:42.009][biodb::testThat]
biodb.INFO [2024-05-04 16:07:42.010][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-04 16:07:42.011][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:42.013][biodb::testThat]
biodb.DEBUG[2024-05-04 16:07:42.016][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2024-05-04 16:07:42.018][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
biodb.TRACE[2024-05-04 16:07:42.020][cch$loadFileContent] Trying to load 8 files from cache: [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.INFO [2024-05-04 16:07:42.022][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8" for "ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8".
biodb.TRACE[2024-05-04 16:07:42.024][cch$loadFileContent] file.exist = [8]: "FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE".
biodb.TRACE[2024-05-04 16:07:42.025][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 16:07:42.027][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 16:07:42.028][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2024-05-04 16:07:42.031][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 16:07:42.032][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2024-05-04 16:07:42.034][private$retrieveContents] Get entry content(s) for 8 id(s)...
biodb.DEBUG[2024-05-04 16:07:42.042][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833%2C3002%2C3627%2C4316%2C50943%2C5551%2C916%2C9606&retmode=xml".
biodb.DEBUG[2024-05-04 16:07:42.060][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 16:07:42.062][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 16:07:42.063][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833%2C3002%2C3627%2C4316%2C50943%2C5551%2C916%2C9606&retmode=xml".
biodb.TRACE[2024-05-04 16:07:42.142][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833%2C3002%2C3627%2C4316%2C50943%2C5551%2C916%2C9606&retmode=xml does not exist.
biodb.TRACE[2024-05-04 16:07:42.143][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 16:07:42.145][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833%2C3002%2C3627%2C4316%2C50943%2C5551%2C916%2C9606&retmode=xml" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 16:07:42.146][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2833%2C3002%2C3627%2C4316%2C50943%2C5551%2C916%2C9606&retmode=xml).
biodb.TRACE[2024-05-04 16:07:43.236][private$doSaveContentToFile] Saving to cache [8]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/2833.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/3002.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/3627.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/4316.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/50943.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/5551.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/916.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/9606.xml"
biodb.INFO [2024-05-04 16:07:43.299][biodb::testThat]
biodb.INFO [2024-05-04 16:07:43.301][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-04 16:07:43.302][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:43.303][biodb::testThat]
biodb.TRACE[2024-05-04 16:07:43.308][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:43.310][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:43.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:43.313][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:43.315][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2024-05-04 16:07:43.329][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2024-05-04 16:07:43.331][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 16:07:43.333][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2833".
biodb.TRACE[2024-05-04 16:07:43.335][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 16:07:43.337][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8/2833.xml".
biodb.DEBUG[2024-05-04 16:07:43.339][conn$getEntryContent] 1 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 16:07:43.341][self$createEntryFromContent] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2024-05-04 16:07:43.343][self$createEntryFromContent] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2024-05-04 16:07:43.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:43.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:43.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:43.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:43.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:43.358][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:43.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:43.362][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2024-05-04 16:07:43.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2024-05-04 16:07:43.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:43.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:43.368][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2024-05-04 16:07:43.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2024-05-04 16:07:43.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:43.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:43.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:43.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:43.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:43.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:43.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:43.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:43.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:43.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:43.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:43.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:43.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:43.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:43.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:43.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:43.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:43.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:43.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:43.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:43.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:43.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:43.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:43.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:43.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:43.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:43.410][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-05-04 16:07:43.411][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-04 16:07:43.570][biodb::testThat]
biodb.INFO [2024-05-04 16:07:43.572][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-04 16:07:43.573][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:43.574][biodb::testThat]
biodb.INFO [2024-05-04 16:07:43.629][biodb::testThat]
biodb.INFO [2024-05-04 16:07:43.630][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-04 16:07:43.631][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:43.633][biodb::testThat]
biodb.INFO [2024-05-04 16:07:43.682][biodb::testThat]
biodb.INFO [2024-05-04 16:07:43.683][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-04 16:07:43.685][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:43.686][biodb::testThat]
biodb.INFO [2024-05-04 16:07:43.702][biodb::testThat]
biodb.INFO [2024-05-04 16:07:43.703][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-04 16:07:43.704][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:43.705][biodb::testThat]
biodb.INFO [2024-05-04 16:07:43.717][biodb::testThat]
biodb.INFO [2024-05-04 16:07:43.719][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-04 16:07:43.721][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:43.722][biodb::testThat]
biodb.DEBUG[2024-05-04 16:07:43.728][function(conn, opt)] Trying to download "https://www.ncbi.nlm.nih.gov/gene?term=2833".
biodb.DEBUG[2024-05-04 16:07:46.475][getUrlContent] Use RCurl for downloading content of URL https://www.ncbi.nlm.nih.gov/gene?term=2833.
biodb.INFO [2024-05-04 16:07:49.789][biodb::testThat]
biodb.INFO [2024-05-04 16:07:49.791][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-04 16:07:49.792][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:49.793][biodb::testThat]
biodb.INFO [2024-05-04 16:07:49.804][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-04 16:07:49.806][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.gene from the request scheduler
biodb.INFO [2024-05-04 16:07:49.807][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.DEBUG[2024-05-04 16:07:49.808][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.ccds from the request scheduler
biodb.INFO [2024-05-04 16:07:49.816][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2024-05-04 16:07:49.817][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-04 16:07:49.819][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:49.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:49.821][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:49.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:49.823][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.824][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.INFO [2024-05-04 16:07:49.830][biodb::testContext]
biodb.INFO [2024-05-04 16:07:49.832][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:07:49.833][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2024-05-04 16:07:49.834][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:07:49.835][biodb::testContext]
biodb.INFO [2024-05-04 16:07:49.838][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:07:49.840][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-04 16:07:49.846][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:07:49.847][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-04 16:07:49.849][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-04 16:07:49.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:49.853][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-04 16:07:49.855][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-04 16:07:49.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.858][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[2024-05-04 16:07:49.860][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-04 16:07:49.861][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-04 16:07:49.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:49.866][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-04 16:07:49.868][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-04 16:07:49.869][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-04 16:07:49.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:49.874][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-04 16:07:49.876][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-04 16:07:49.877][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-04 16:07:49.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:49.882][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-04 16:07:49.884][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-04 16:07:49.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:49.889][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-04 16:07:49.891][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-04 16:07:49.892][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-04 16:07:49.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:49.897][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-04 16:07:49.899][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-04 16:07:49.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.903][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[2024-05-04 16:07:49.904][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-04 16:07:49.906][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-04 16:07:49.907][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-04 16:07:49.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:49.913][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:07:49.914][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-04 16:07:49.916][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-04 16:07:49.917][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-04 16:07:49.918][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-04 16:07:49.920][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-04 16:07:49.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:49.925][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-04 16:07:49.927][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-04 16:07:49.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:49.932][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-04 16:07:49.967][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-04 16:07:49.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:49.974][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-04 16:07:49.975][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-04 16:07:49.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:49.980][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-04 16:07:49.981][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-04 16:07:49.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:49.986][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-04 16:07:49.987][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-04 16:07:49.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:49.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:49.992][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:07:49.993][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-04 16:07:49.997][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-04 16:07:49.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:49.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.002][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-04 16:07:50.003][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-04 16:07:50.004][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-04 16:07:50.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.009][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-04 16:07:50.011][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.013][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-04 16:07:50.014][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.015][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:50.016][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.018][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.019][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.020][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.021][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:07:50.023][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:50.024][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.025][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-04 16:07:50.026][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:50.028][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.029][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.030][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:07:50.030][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:07:50.030][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:07:50.030][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:07:50.030][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:07:50.032][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:50.033][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.034][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.035][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:50.037][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.038][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.039][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.040][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.041][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:50.042][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:50.044][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.045][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.046][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-04 16:07:50.048][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.050][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:07:50.051][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.052][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:50.054][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.055][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.056][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.057][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.059][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:07:50.060][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:50.061][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.062][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-04 16:07:50.064][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:50.065][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.066][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.068][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:07:50.068][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:07:50.068][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:07:50.068][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:07:50.068][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:07:50.069][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:50.070][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.071][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.072][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:50.074][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.076][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.077][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.079][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:50.080][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:50.081][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.082][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.084][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-04 16:07:50.086][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.087][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-04 16:07:50.088][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.089][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:50.091][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.092][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.093][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.095][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.096][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:07:50.097][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:50.098][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.100][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-04 16:07:50.101][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:50.102][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.103][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.105][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.106][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:50.107][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.108][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.109][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:50.110][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.112][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.114][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.115][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.116][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:50.117][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:50.118][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.120][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.121][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-04 16:07:50.123][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.124][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:07:50.126][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.127][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:50.128][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.129][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.130][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.132][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.133][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:07:50.134][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:50.136][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.137][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-04 16:07:50.138][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:50.139][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.141][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.142][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.143][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:50.145][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.146][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.147][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:50.148][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.149][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.151][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.152][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.153][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:50.154][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:50.155][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.157][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.158][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:07:50.160][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.167][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[2024-05-04 16:07:50.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.173][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[2024-05-04 16:07:50.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.191][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[2024-05-04 16:07:50.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.202][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[2024-05-04 16:07:50.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.225][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[2024-05-04 16:07:50.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.259][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-04 16:07:50.260][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-04 16:07:50.262][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-04 16:07:50.264][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-04 16:07:50.266][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 16:07:50.268][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-04 16:07:50.270][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-04 16:07:50.271][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-04 16:07:50.273][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 16:07:50.275][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-04 16:07:50.279][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 16:07:50.281][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-04 16:07:50.283][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-04 16:07:50.285][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-04 16:07:50.287][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 16:07:50.288][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 16:07:50.290][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-04 16:07:50.292][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-04 16:07:50.294][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 16:07:50.295][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-04 16:07:50.297][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-04 16:07:50.299][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-04 16:07:50.301][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-04 16:07:50.302][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-04 16:07:50.304][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-04 16:07:50.306][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-04 16:07:50.308][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-04 16:07:50.309][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-04 16:07:50.311][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-04 16:07:50.313][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-04 16:07:50.314][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-04 16:07:50.316][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-04 16:07:50.318][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-04 16:07:50.319][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-04 16:07:50.321][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-04 16:07:50.323][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-04 16:07:50.325][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-04 16:07:50.326][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-04 16:07:50.328][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-04 16:07:50.330][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-04 16:07:50.331][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-04 16:07:50.333][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-04 16:07:50.335][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-04 16:07:50.337][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-04 16:07:50.338][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-04 16:07:50.340][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 16:07:50.342][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-04 16:07:50.344][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-04 16:07:50.345][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-04 16:07:50.347][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-04 16:07:50.348][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-04 16:07:50.350][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-04 16:07:50.352][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-04 16:07:50.353][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-04 16:07:50.355][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-04 16:07:50.357][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-04 16:07:50.359][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-04 16:07:50.367][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-04 16:07:50.369][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-04 16:07:50.370][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-04 16:07:50.372][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-04 16:07:50.373][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-04 16:07:50.375][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-04 16:07:50.377][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-04 16:07:50.378][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-04 16:07:50.380][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-04 16:07:50.381][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 16:07:50.383][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 16:07:50.384][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-04 16:07:50.386][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-04 16:07:50.387][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-04 16:07:50.389][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-04 16:07:50.391][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-04 16:07:50.392][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-04 16:07:50.394][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-04 16:07:50.395][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-04 16:07:50.397][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-04 16:07:50.398][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-04 16:07:50.400][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-04 16:07:50.401][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-04 16:07:50.403][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-04 16:07:50.405][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-04 16:07:50.406][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-04 16:07:50.408][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-04 16:07:50.410][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:07:50.411][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:07:50.412][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.415][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.416][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[2024-05-04 16:07:50.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.423][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[2024-05-04 16:07:50.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.431][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[2024-05-04 16:07:50.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.446][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[2024-05-04 16:07:50.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:50.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:50.549][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2024-05-04 16:07:50.551][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2024-05-04 16:07:50.553][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.555][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2024-05-04 16:07:50.556][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.557][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:50.558][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.559][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.561][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.562][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.563][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2024-05-04 16:07:50.564][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:50.565][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.567][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2024-05-04 16:07:50.568][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:50.569][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2024-05-04 16:07:50.569][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2024-05-04 16:07:50.570][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.571][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.573][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 16:07:50.574][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.575][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.576][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:50.577][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.578][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.580][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.581][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2024-05-04 16:07:50.581][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2024-05-04 16:07:50.582][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:50.583][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:50.584][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.585][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.587][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2024-05-04 16:07:50.589][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.590][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2024-05-04 16:07:50.591][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.592][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:50.594][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.595][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.596][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.597][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.598][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 16:07:50.600][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:50.601][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.602][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2024-05-04 16:07:50.603][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:50.604][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2024-05-04 16:07:50.604][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2024-05-04 16:07:50.604][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2024-05-04 16:07:50.604][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2024-05-04 16:07:50.604][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2024-05-04 16:07:50.604][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2024-05-04 16:07:50.606][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.607][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:07:50.608][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 16:07:50.609][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.610][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.612][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:50.613][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.614][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.615][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.616][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2024-05-04 16:07:50.616][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2024-05-04 16:07:50.617][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:50.619][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:50.620][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.621][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.622][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2024-05-04 16:07:50.624][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.626][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2024-05-04 16:07:50.627][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.628][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:50.629][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.630][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.632][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.633][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.634][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 16:07:50.635][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:50.637][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.638][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2024-05-04 16:07:50.639][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:50.640][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2024-05-04 16:07:50.640][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:50.640][self$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[2024-05-04 16:07:50.640][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:50.640][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:50.640][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:50.640][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:50.640][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:50.640][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:50.640][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:50.640][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2024-05-04 16:07:50.640][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:50.640][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:50.640][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:07:50.642][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.643][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:07:50.643][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:07:50.643][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:07:50.644][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2024-05-04 16:07:50.645][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.646][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.647][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:50.649][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.650][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.651][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.652][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2024-05-04 16:07:50.652][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2024-05-04 16:07:50.652][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2024-05-04 16:07:50.653][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:50.654][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:50.656][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.657][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2024-05-04 16:07:50.658][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2024-05-04 16:07:50.660][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.662][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2024-05-04 16:07:50.663][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.664][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:50.665][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.666][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.667][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.669][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.670][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 16:07:50.671][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:50.672][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.674][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2024-05-04 16:07:50.675][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:50.676][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2024-05-04 16:07:50.676][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2024-05-04 16:07:50.677][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:50.678][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:50.680][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2024-05-04 16:07:50.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.683][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:50.684][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:50.685][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:50.686][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:50.688][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2024-05-04 16:07:50.688][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2024-05-04 16:07:50.688][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2024-05-04 16:07:50.689][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:50.690][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:50.691][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:50.692][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2024-05-04 16:07:50.694][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2024-05-04 16:07:50.696][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 16:07:50.697][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 16:07:50.699][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2024-05-04 16:07:50.701][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 16:07:50.702][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2024-05-04 16:07:50.709][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2024-05-04 16:07:50.710][super$initialize] Register connector ncbi.pubchem.comp with the request scheduler
biodb.DEBUG[2024-05-04 16:07:50.712][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.pubchem.comp.
biodb.DEBUG[2024-05-04 16:07:50.714][private$addConnectorRules] Create new rule for URL "pubchem.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.comp".
biodb.DEBUG[2024-05-04 16:07:50.715][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2024-05-04 16:07:50.716][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2024-05-04 16:07:50.718][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.comp".
biodb.DEBUG[2024-05-04 16:07:50.720][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2024-05-04 16:07:50.721][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2024-05-04 16:07:50.722][rule$addConnector] Connector "ncbi.pubchem.comp" is already listed in rule "pubchem.ncbi.nlm.nih.gov".
biodb.DEBUG[2024-05-04 16:07:50.728][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2024-05-04 16:07:50.733][biodb::testThat]
biodb.INFO [2024-05-04 16:07:50.734][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-04 16:07:50.736][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:50.743][biodb::testThat]
biodb.TRACE[2024-05-04 16:07:50.748][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2024-05-04 16:07:50.749][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2024-05-04 16:07:50.752][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2024-05-04 16:07:50.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:50.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:50.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:50.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:50.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:50.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:50.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:50.771][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:50.773][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:50.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.775][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:50.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:50.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.782][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:50.783][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:50.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.786][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.787][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:50.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:50.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.792][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:50.794][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:50.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.796][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.798][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:50.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:50.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.803][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:50.804][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:50.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.806][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.808][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:50.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:50.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.813][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:50.814][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:50.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.816][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.818][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:50.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:50.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.824][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:50.825][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:50.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.827][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.829][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:50.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:50.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.834][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:50.835][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:50.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.837][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.839][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:50.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:50.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.844][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:50.845][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:50.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.848][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.849][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:50.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:50.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.855][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:50.856][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:50.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.858][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:50.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:50.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.865][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:50.866][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:50.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.868][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.870][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:50.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:50.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.875][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:50.876][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:50.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.878][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.880][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:50.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:50.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.885][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:50.886][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:50.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.888][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:50.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:50.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.895][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:50.896][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:50.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.898][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.900][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:50.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:50.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.905][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:50.906][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:50.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.908][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.910][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:50.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:50.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.915][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2024-05-04 16:07:50.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:50.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.920][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:50.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:50.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.925][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:50.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:50.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.929][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2024-05-04 16:07:50.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:50.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.934][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:50.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:50.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.939][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:50.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:50.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.944][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2024-05-04 16:07:50.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:50.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.949][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:50.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:50.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.954][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:50.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:50.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.959][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2024-05-04 16:07:50.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:50.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.965][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:50.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:50.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.969][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:50.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:50.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.974][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2024-05-04 16:07:50.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:50.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.979][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:50.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:50.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.984][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:50.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:50.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.989][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:50.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:50.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.994][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:50.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:50.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:50.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:50.999][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:51.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:51.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.009][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:51.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:51.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:51.043][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2024-05-04 16:07:51.046][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:51.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:51.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.051][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:51.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:51.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.056][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:51.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:51.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.061][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:51.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:51.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.066][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:51.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:51.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.071][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:51.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:51.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.076][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:51.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:51.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.094][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:51.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:51.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.143][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:51.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:51.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.148][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:51.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:51.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.153][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:51.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:51.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.183][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.184][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.187][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.203][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:51.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:51.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:51.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:51.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:51.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:51.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.218][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:51.219][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:51.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.222][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.223][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:51.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:51.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:51.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:51.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:51.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:51.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:51.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:51.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.253][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:51.254][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:51.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.256][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:51.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:51.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.272][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:51.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:51.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.277][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:51.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:51.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.282][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:51.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:51.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.287][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:51.289][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:51.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.291][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.292][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:51.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:51.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.307][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:51.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:51.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.312][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:51.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:51.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.317][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:51.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:51.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.322][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:51.323][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:51.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.326][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.327][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:51.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:51.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.342][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:51.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:51.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.347][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:51.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:51.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.351][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:51.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:51.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.356][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:51.358][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:51.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.360][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.361][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:51.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:51.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.376][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:51.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:51.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.381][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:51.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:51.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.386][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:51.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:51.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.390][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:51.392][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:51.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.394][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.395][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:51.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:51.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.410][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.415][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.420][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.425][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.426][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.428][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.429][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.444][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.449][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.454][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.459][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.460][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.462][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.464][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.479][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.484][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.489][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.493][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.495][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.497][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.513][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.518][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.523][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.528][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.536][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.538][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.554][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.559][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.564][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.568][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.570][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.572][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.573][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.588][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:51.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:51.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.593][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:51.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:51.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:51.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:51.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.602][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:51.604][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:51.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.606][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.607][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:51.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:51.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.627][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.632][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.637][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.638][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.641][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.657][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:51.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:51.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:51.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:51.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:51.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:51.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.672][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:51.673][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:51.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.676][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.677][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:51.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:51.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.691][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.693][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.696][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.703][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.704][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.707][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.713][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.715][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.717][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.724][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.725][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.728][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.734][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.736][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.738][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.745][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.746][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.749][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.755][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:51.757][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:51.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.759][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.766][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:51.767][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:51.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.770][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.776][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.777][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.780][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.786][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:51.788][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:51.789][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.790][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.797][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:51.798][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:51.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.800][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.807][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:51.808][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:51.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.810][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.818][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:51.820][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:51.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.822][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.829][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:51.830][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:51.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.832][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.839][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:51.841][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:51.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.843][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.851][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2024-05-04 16:07:51.852][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2024-05-04 16:07:51.854][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2024-05-04 16:07:51.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:51.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:51.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:51.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:51.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:51.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:51.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:51.872][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.873][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.875][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:51.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:51.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.882][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.883][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.885][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.887][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:51.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.892][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.893][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.895][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.897][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:51.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.902][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.903][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.905][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.907][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:51.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.912][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.913][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.915][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.917][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:51.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.922][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.923][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.925][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.927][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:51.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.932][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:51.933][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:51.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.936][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.937][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:51.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:51.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.949][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:51.950][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:51.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.952][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.954][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:51.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:51.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.959][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:51.960][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:51.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.962][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:51.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:51.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.969][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.971][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.973][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.974][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:51.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.979][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:51.981][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:51.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.983][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.984][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:51.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:51.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.989][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:51.991][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:51.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.993][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:51.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:51.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:51.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:51.999][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.001][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.003][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.004][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.009][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.011][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.013][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.014][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.019][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2024-05-04 16:07:52.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.024][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.029][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.034][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2024-05-04 16:07:52.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.039][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.044][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.049][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2024-05-04 16:07:52.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.054][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.059][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.064][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2024-05-04 16:07:52.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.068][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.073][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.078][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2024-05-04 16:07:52.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.083][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.088][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.092][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:52.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:52.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.097][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:52.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:52.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.102][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:52.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:52.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.112][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:52.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:52.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:52.146][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2024-05-04 16:07:52.148][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:52.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:52.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.153][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:52.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:52.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.158][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:52.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:52.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.163][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:52.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:52.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.168][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:52.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:52.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.173][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:52.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:52.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.178][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:52.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:52.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.195][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:52.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:52.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.236][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:52.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:52.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.241][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:52.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:52.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.246][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:52.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:52.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.276][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.277][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.279][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:52.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:52.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:52.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:52.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:52.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:52.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.310][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:52.311][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:52.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.314][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:52.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:52.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:52.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:52.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:52.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:52.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:52.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:52.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.351][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:52.352][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:52.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.354][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:52.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:52.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.370][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:52.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:52.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.375][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:52.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:52.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.380][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:52.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:52.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.385][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:52.386][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:52.388][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.389][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.390][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:52.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:52.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.405][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:52.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:52.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.410][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:52.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:52.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.415][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:52.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:52.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.419][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:52.421][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:52.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.423][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.424][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:52.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:52.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.439][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.444][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.449][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.454][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.455][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.458][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.459][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.474][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.479][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.484][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.489][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.490][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.492][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.494][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.508][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:52.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:52.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:52.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:52.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:52.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:52.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.523][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:52.525][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:52.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.527][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.528][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:52.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:52.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:52.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:52.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:52.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:52.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:52.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:52.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.558][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:52.559][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:52.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.561][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.562][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:52.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:52.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.577][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.582][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.587][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.592][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.593][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.595][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.596][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.611][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.616][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.621][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.625][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.627][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.628][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.629][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.630][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.645][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.650][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.655][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.660][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.661][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.663][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.665][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.680][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.685][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.690][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.695][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.696][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.698][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.700][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.715][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.726][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.731][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.736][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.737][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.739][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.741][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:52.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:52.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:52.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:52.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:52.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:52.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.770][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:52.772][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:52.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.774][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:52.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:52.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.790][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:52.791][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:52.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.794][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.800][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.802][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:52.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.804][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.811][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.812][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:52.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.814][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.821][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.823][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:52.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.825][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.832][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.833][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:52.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.835][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.842][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.844][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:52.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.846][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.853][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:52.854][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:52.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.856][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.863][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:52.864][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:52.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.866][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.873][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:52.874][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:52.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.876][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.883][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:52.884][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:52.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.887][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.893][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:52.895][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:52.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.897][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.904][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:52.905][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:52.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.907][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.914][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:52.915][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:52.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.917][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.924][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.925][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:52.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.928][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:52.934][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.936][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:52.937][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:52.938][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 16:07:52.950][biodb::testThat]
biodb.INFO [2024-05-04 16:07:52.951][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-04 16:07:52.952][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:52.953][biodb::testThat]
biodb.DEBUG[2024-05-04 16:07:52.956][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2024-05-04 16:07:52.958][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-04 16:07:52.962][cch$loadFileContent] Trying to load 2 files from cache: [2]: "2, 65124".
biodb.TRACE[2024-05-04 16:07:52.964][cch$loadFileContent] file.exist = [2]: "FALSE, TRUE".
biodb.TRACE[2024-05-04 16:07:52.977][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/65124.xml".
biodb.DEBUG[2024-05-04 16:07:52.979][conn$getEntryContent] 1 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 16:07:52.980][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2024-05-04 16:07:52.981][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 16:07:52.983][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2024-05-04 16:07:52.984][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.DEBUG[2024-05-04 16:07:52.986][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2/XML".
biodb.DEBUG[2024-05-04 16:07:52.988][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 16:07:52.990][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 16:07:52.991][private$doSendRequestOnce] Sent URL is "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2/XML".
biodb.TRACE[2024-05-04 16:07:53.080][getRCurlRequestResult] Using RCurl package for sending request (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2/XML).
biodb.TRACE[2024-05-04 16:07:53.177][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/2.xml"
biodb.DEBUG[2024-05-04 16:07:53.180][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 16:07:53.181][self$createEntryFromContent] Creating PubChem Compound entries from 2 content(s).
biodb.DEBUG[2024-05-04 16:07:53.183][self$createEntryFromContent] Parsing 2 PubChem Compound entries.
biodb.DEBUG[2024-05-04 16:07:53.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:53.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:53.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:53.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:53.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:53.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:53.197][FUN] Functions in observer BiodbConfig: [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[2024-05-04 16:07:53.200][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.201][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.204][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.210][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.212][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.214][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.216][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.221][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.222][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.224][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.226][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.231][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.232][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.234][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.236][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.241][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.242][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.245][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.246][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.251][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.253][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.255][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.256][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.261][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:53.263][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:53.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.265][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.267][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:53.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:53.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.272][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:53.273][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:53.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.275][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.277][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:53.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:53.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.282][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:53.283][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:53.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.285][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.287][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:53.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:53.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.292][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:53.293][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:53.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.296][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:53.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:53.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.302][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:53.304][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:53.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.306][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.308][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:53.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:53.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.313][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:53.314][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:53.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.316][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:53.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:53.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.331][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:53.332][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:53.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.334][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.336][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:53.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:53.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.341][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:53.342][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:53.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.345][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.346][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:53.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:53.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.351][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2024-05-04 16:07:53.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.356][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.361][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.366][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2024-05-04 16:07:53.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.371][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.376][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.381][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2024-05-04 16:07:53.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.386][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.391][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.395][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2024-05-04 16:07:53.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.400][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.405][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.410][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2024-05-04 16:07:53.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.415][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.420][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.425][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:53.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:53.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.430][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:53.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:53.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.435][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:53.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:53.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.445][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:53.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:53.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:53.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:53.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:53.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:53.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:53.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:53.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:53.478][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.TRACE[2024-05-04 16:07:53.481][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.482][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.484][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.485][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.491][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.493][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.495][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.497][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.502][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.503][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.505][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.507][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.512][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.513][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.516][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.517][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.522][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.524][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.526][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.528][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.533][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.534][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.536][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.538][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.543][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:53.544][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:53.546][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.547][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.548][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:53.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:53.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.553][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:53.555][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:53.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.557][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.559][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:53.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:53.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.564][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:53.565][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:53.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.567][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.569][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:53.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:53.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.574][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:53.575][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:53.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.578][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:53.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:53.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.584][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:53.586][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:53.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.588][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.589][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:53.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:53.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.595][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:53.596][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:53.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.598][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:53.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:53.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.605][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:53.606][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:53.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.609][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.610][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:53.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:53.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.615][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:53.617][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:53.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.619][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.621][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:53.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:53.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.626][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2024-05-04 16:07:53.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.631][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.636][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:53.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.641][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2024-05-04 16:07:53.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.646][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.650][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:53.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.656][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2024-05-04 16:07:53.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.660][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.665][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:53.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.670][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2024-05-04 16:07:53.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.675][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.680][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:53.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.685][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2024-05-04 16:07:53.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.690][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.695][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:53.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.700][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:53.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:53.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.705][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:53.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:53.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.716][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:53.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:53.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.726][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:53.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:53.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:53.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:53.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:53.776][self$createEntryFromContent] Accession numbers: 2, 65124.
biodb.TRACE[2024-05-04 16:07:53.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-04 16:07:53.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-04 16:07:53.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-04 16:07:53.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-04 16:07:53.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-04 16:07:53.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-04 16:07:53.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-04 16:07:53.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-04 16:07:53.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-04 16:07:53.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-04 16:07:53.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-04 16:07:53.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-04 16:07:53.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 16:07:53.826][biodb::testThat]
biodb.INFO [2024-05-04 16:07:53.827][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-04 16:07:53.828][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:53.829][biodb::testThat]
biodb.TRACE[2024-05-04 16:07:53.833][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:53.834][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:53.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.837][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:53.838][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.TRACE[2024-05-04 16:07:53.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:53.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:53.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:53.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:53.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:53.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:53.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:53.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:53.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:53.874][function(conn, opt)] With value "(2-acetyloxy-3-carboxypropyl)-trimethylazanium".
biodb.DEBUG[2024-05-04 16:07:53.881][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term="(2-acetyloxy-3-carboxypropyl)-trimethylazanium"[IUPACName]&retmax=10".
biodb.DEBUG[2024-05-04 16:07:53.885][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 16:07:53.886][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 16:07:53.888][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=%22%282-acetyloxy-3-carboxypropyl%29-trimethylazanium%22%5BIUPACName%5D&retmax=10".
biodb.TRACE[2024-05-04 16:07:53.945][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=%22%282-acetyloxy-3-carboxypropyl%29-trimethylazanium%22%5BIUPACName%5D&retmax=10 does not exist.
biodb.TRACE[2024-05-04 16:07:53.947][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 16:07:53.948][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=%22%282-acetyloxy-3-carboxypropyl%29-trimethylazanium%22%5BIUPACName%5D&retmax=10" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 16:07:53.950][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=%22%282-acetyloxy-3-carboxypropyl%29-trimethylazanium%22%5BIUPACName%5D&retmax=10).
biodb.DEBUG[2024-05-04 16:07:54.389][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 16:07:54.393][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/0c7e343368bb974cc0f019187ff4a141.content"
biodb.TRACE[2024-05-04 16:07:54.398][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/0c7e343368bb974cc0f019187ff4a141.request"
biodb.DEBUG[2024-05-04 16:07:54.401][function(conn, opt)] With found IDs [5]: "87229113, 25217148, 450343, 450342, 2".
biodb.TRACE[2024-05-04 16:07:54.420][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:54.422][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:54.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.424][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.425][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:54.427][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:54.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.429][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 16:07:54.436][biodb::testThat]
biodb.INFO [2024-05-04 16:07:54.437][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-04 16:07:54.438][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:54.439][biodb::testThat]
biodb.TRACE[2024-05-04 16:07:54.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:54.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:54.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:54.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:54.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:54.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:54.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:54.512][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[2024-05-04 16:07:54.516][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 16:07:54.517][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0c7e343368bb974cc0f019187ff4a141".
biodb.TRACE[2024-05-04 16:07:54.519][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 16:07:54.521][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/0c7e343368bb974cc0f019187ff4a141.content".
biodb.INFO [2024-05-04 16:07:54.539][biodb::testThat]
biodb.INFO [2024-05-04 16:07:54.541][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-04 16:07:54.542][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:54.543][biodb::testThat]
biodb.TRACE[2024-05-04 16:07:54.556][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:54.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:54.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.561][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:54.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:54.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.567][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:54.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:54.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.571][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:54.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:54.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.576][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:54.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:54.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.581][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:54.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:54.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.586][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:54.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:54.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.610][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:54.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:54.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.616][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:07:54.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:07:54.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.621][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:54.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:07:54.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.626][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:54.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:54.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.631][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:54.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:54.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.636][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:54.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:54.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:54.641][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:54.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:54.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:54.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 16:07:54.737][biodb::testThat]
biodb.INFO [2024-05-04 16:07:54.739][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-04 16:07:54.740][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:54.741][biodb::testThat]
biodb.INFO [2024-05-04 16:07:54.753][biodb::testThat]
biodb.INFO [2024-05-04 16:07:54.754][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-04 16:07:54.755][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:54.757][biodb::testThat]
biodb.INFO [2024-05-04 16:07:54.769][biodb::testThat]
biodb.INFO [2024-05-04 16:07:54.770][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-04 16:07:54.771][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:54.772][biodb::testThat]
biodb.DEBUG[2024-05-04 16:07:54.777][function(conn, opt)] Trying to download "https://pubchem.ncbi.nlm.nih.gov/compound/2".
biodb.DEBUG[2024-05-04 16:07:54.875][getUrlContent] Use RCurl for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/compound/2.
biodb.INFO [2024-05-04 16:07:54.989][biodb::testThat]
biodb.INFO [2024-05-04 16:07:54.990][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-04 16:07:54.991][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:54.993][biodb::testThat]
biodb.DEBUG[2024-05-04 16:07:55.052][getUrlContent] Use RCurl for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=2&t=l.
biodb.TRACE[2024-05-04 16:07:55.115][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:55.117][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:55.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.119][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.120][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.122][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.124][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 16:07:55.126][biodb::testThat]
biodb.INFO [2024-05-04 16:07:55.128][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-05-04 16:07:55.129][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:55.130][biodb::testThat]
biodb.TRACE[2024-05-04 16:07:55.147][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:55.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:55.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.152][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:55.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:55.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:55.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:55.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:55.259][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[2024-05-04 16:07:55.263][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 16:07:55.264][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0c7e343368bb974cc0f019187ff4a141".
biodb.TRACE[2024-05-04 16:07:55.266][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 16:07:55.268][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/0c7e343368bb974cc0f019187ff4a141.content".
biodb.INFO [2024-05-04 16:07:55.289][biodb::testThat]
biodb.INFO [2024-05-04 16:07:55.290][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-04 16:07:55.291][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:55.292][biodb::testThat]
biodb.TRACE[2024-05-04 16:07:55.296][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 16:07:55.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 16:07:55.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.301][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 16:07:55.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 16:07:55.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:55.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:55.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:55.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:55.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:55.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:55.369][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:55.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:55.379][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[2024-05-04 16:07:55.383][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 16:07:55.385][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2616ca37a6f6e1bc281f8c51bc53ce81".
biodb.TRACE[2024-05-04 16:07:55.386][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 16:07:55.398][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/2616ca37a6f6e1bc281f8c51bc53ce81.content".
biodb.DEBUG[2024-05-04 16:07:55.400][private$loadEntries] Creating entries from ids [3]: "171364948, 171334113, 171326497".
biodb.DEBUG[2024-05-04 16:07:55.401][conn$getEntryContent] Get PubChem Compound entry content(s) for 3 id(s)...
biodb.TRACE[2024-05-04 16:07:55.403][cch$loadFileContent] Trying to load 3 files from cache: [3]: "171364948, 171334113, 171326497".
biodb.TRACE[2024-05-04 16:07:55.405][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2024-05-04 16:07:55.437][loadFileContents] Loaded 3 files from cache: [3]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/171364948.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/171334113.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/171326497.xml".
biodb.DEBUG[2024-05-04 16:07:55.439][conn$getEntryContent] 3 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 16:07:55.441][self$createEntryFromContent] Creating PubChem Compound entries from 3 content(s).
biodb.DEBUG[2024-05-04 16:07:55.442][self$createEntryFromContent] Parsing 3 PubChem Compound entries.
biodb.DEBUG[2024-05-04 16:07:55.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:55.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:55.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:55.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:55.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:55.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:55.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:55.460][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:55.461][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:55.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.463][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:55.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:55.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.469][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.471][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.473][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.475][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.480][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.481][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.483][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.485][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.490][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.491][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.493][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.495][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.500][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.501][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.504][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.505][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.510][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.511][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.514][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.515][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.520][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:55.521][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:55.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.524][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.525][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:55.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:55.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.530][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:55.532][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:55.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.534][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.535][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:55.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:55.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.540][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:55.542][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:55.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.544][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:55.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:55.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.550][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:55.552][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:55.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.554][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:55.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:55.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.560][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:55.562][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:55.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.564][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.566][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:55.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:55.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.570][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:55.572][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.574][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:55.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.581][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:55.582][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:55.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.584][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.586][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:55.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:55.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.591][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:55.592][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:55.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.595][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:55.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:55.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.601][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2024-05-04 16:07:55.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.606][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.611][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.616][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2024-05-04 16:07:55.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.621][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.626][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.631][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2024-05-04 16:07:55.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.636][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.641][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.645][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2024-05-04 16:07:55.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.650][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.655][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.660][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2024-05-04 16:07:55.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.665][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.670][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.675][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:55.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:55.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.680][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:55.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:55.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.685][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:55.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:55.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:55.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:55.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.695][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:55.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:55.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:55.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:55.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:55.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:55.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:55.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:55.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:55.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:55.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:55.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:55.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:55.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:55.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:55.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:55.730][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:55.732][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:55.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.734][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:55.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:55.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.740][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.742][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.744][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.746][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.751][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.752][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.754][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.756][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.761][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.762][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.765][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.766][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.778][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.779][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.781][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.783][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.788][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.789][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.792][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.793][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.798][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:55.799][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:55.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.802][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.803][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:55.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:55.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.808][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:55.809][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:55.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.812][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.813][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:55.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:55.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.818][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:55.819][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:55.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.822][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.823][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:55.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:55.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.828][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:55.829][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:55.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.832][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.833][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:55.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:55.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.838][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:55.839][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:55.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.841][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.843][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:55.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:55.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.848][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:55.849][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.851][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:55.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:55.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.858][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:55.859][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:55.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.861][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.863][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:55.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:55.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.868][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:55.869][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:55.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.872][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.873][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:55.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:55.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.878][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2024-05-04 16:07:55.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.883][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.888][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:55.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.893][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2024-05-04 16:07:55.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.898][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.902][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:55.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.907][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2024-05-04 16:07:55.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.912][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.917][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:55.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.921][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2024-05-04 16:07:55.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.926][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.931][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:55.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.936][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2024-05-04 16:07:55.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.941][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.946][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:55.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:55.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:55.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.955][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:55.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:55.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.960][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:55.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:55.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:55.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:55.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.970][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:55.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:55.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:55.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:55.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:55.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:55.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:55.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:55.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:55.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:55.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:55.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:55.991][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:55.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:56.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:56.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:56.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:56.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:56.006][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.007][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.010][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.016][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:56.017][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:56.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.020][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.021][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:56.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:56.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.026][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:56.028][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:56.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.030][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.032][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:56.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:56.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.037][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:56.038][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:56.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.040][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.042][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:56.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:56.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.047][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:56.048][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:56.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.050][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.052][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:56.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:56.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.057][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:56.058][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:56.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.060][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.062][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:56.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:56.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.067][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:56.068][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:56.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.071][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.072][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:56.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:56.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.077][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:56.079][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:56.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.081][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.083][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:56.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:56.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.088][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:56.089][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:56.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.091][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:56.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:56.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.098][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:56.099][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:56.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.102][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.103][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:56.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:56.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.108][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:56.109][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:56.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.112][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.113][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:56.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:56.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.118][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:56.119][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:56.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.122][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:56.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:56.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.128][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:56.129][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:56.131][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.132][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.133][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:56.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:56.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.138][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:56.140][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:56.141][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.142][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.143][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:56.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:56.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.154][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2024-05-04 16:07:56.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:56.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.159][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:56.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:56.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.164][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:56.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:56.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.169][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2024-05-04 16:07:56.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:56.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.174][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:56.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:56.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.179][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:56.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:56.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.184][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2024-05-04 16:07:56.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:56.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.188][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:56.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:56.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.193][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:56.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:56.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.198][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2024-05-04 16:07:56.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:56.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.203][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:56.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:56.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.208][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:56.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:56.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.212][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2024-05-04 16:07:56.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:56.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.217][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:56.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:56.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.222][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:56.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:56.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:56.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:56.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.232][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.236][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.246][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:56.309][self$createEntryFromContent] Accession numbers: 171364948, 171334113, 171326497.
biodb.DEBUG[2024-05-04 16:07:56.318][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 16:07:56.320][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:56.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:56.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:56.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:56.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:56.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:56.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:56.334][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.339][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.343][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:56.345][private$selectFields]
biodb.TRACE[2024-05-04 16:07:56.346][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:07:56.347][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:07:56.348][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:56.349][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.351][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.353][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.354][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.355][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.358][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.359][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:56.360][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:56.361][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.363][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.365][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.366][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2024-05-04 16:07:56.367][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.372][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.377][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.390][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [171364948].
biodb.DEBUG[2024-05-04 16:07:56.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:56.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:56.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:56.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:56.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:56.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:56.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:56.406][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.411][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.416][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:56.417][private$selectFields]
biodb.TRACE[2024-05-04 16:07:56.418][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:07:56.419][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:07:56.420][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:56.421][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.423][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.425][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.426][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.428][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.430][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.431][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:56.432][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:56.433][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.435][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.437][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.438][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2024-05-04 16:07:56.440][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.444][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.449][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.454][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [171334113].
biodb.DEBUG[2024-05-04 16:07:56.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:56.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:56.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:56.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:56.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:56.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:56.468][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.TRACE[2024-05-04 16:07:56.470][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.475][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.480][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:56.481][private$selectFields]
biodb.TRACE[2024-05-04 16:07:56.482][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:07:56.483][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:07:56.484][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:56.485][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.487][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.489][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.490][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.492][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.494][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.495][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:56.496][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:56.498][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.499][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.501][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.502][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2024-05-04 16:07:56.504][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.514][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.519][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:56.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.524][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [171326497].
biodb.DEBUG[2024-05-04 16:07:56.526][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 16:07:56.527][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.DEBUG[2024-05-04 16:07:56.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:56.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:56.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:56.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:56.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:56.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:56.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:56.549][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[2024-05-04 16:07:56.553][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 16:07:56.554][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 16:07:56.568][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2024-05-04 16:07:56.618][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2024-05-04 16:07:56.620][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 16:07:56.622][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 16:07:56.623][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18%3A226.2%5BMolecularWeight%5D&retmax=3).
biodb.DEBUG[2024-05-04 16:07:56.664][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 16:07:56.667][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/69c19f6998e271aebdcd09a030d9b450.content"
biodb.TRACE[2024-05-04 16:07:56.677][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/69c19f6998e271aebdcd09a030d9b450.request"
biodb.DEBUG[2024-05-04 16:07:56.681][private$loadEntries] Creating entries from ids [3]: "171341956, 171316324, 171316323".
biodb.DEBUG[2024-05-04 16:07:56.683][conn$getEntryContent] Get PubChem Compound entry content(s) for 3 id(s)...
biodb.TRACE[2024-05-04 16:07:56.685][cch$loadFileContent] Trying to load 3 files from cache: [3]: "171341956, 171316324, 171316323".
biodb.TRACE[2024-05-04 16:07:56.687][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-05-04 16:07:56.688][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 16:07:56.690][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 16:07:56.691][conn$getEntryContent] 3 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2024-05-04 16:07:56.692][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 16:07:56.693][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2024-05-04 16:07:56.709][private$retrieveContents] Get entry content(s) for 3 id(s)...
biodb.DEBUG[2024-05-04 16:07:56.712][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/171341956,171316324,171316323/XML".
biodb.DEBUG[2024-05-04 16:07:56.714][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 16:07:56.716][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 16:07:56.717][private$doSendRequestOnce] Sent URL is "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/171341956,171316324,171316323/XML".
biodb.TRACE[2024-05-04 16:07:56.792][getRCurlRequestResult] Using RCurl package for sending request (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/171341956,171316324,171316323/XML).
biodb.TRACE[2024-05-04 16:07:56.930][private$doSaveContentToFile] Saving to cache [3]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/171341956.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/171316324.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/171316323.xml"
biodb.DEBUG[2024-05-04 16:07:56.935][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 16:07:56.936][self$createEntryFromContent] Creating PubChem Compound entries from 3 content(s).
biodb.DEBUG[2024-05-04 16:07:56.938][self$createEntryFromContent] Parsing 3 PubChem Compound entries.
biodb.DEBUG[2024-05-04 16:07:56.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:56.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:56.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:56.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:56.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:56.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:56.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:56.956][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.957][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.960][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:56.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:56.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.966][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:56.968][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:56.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.970][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.972][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:56.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:56.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.980][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:56.982][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:56.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.984][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.986][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:56.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:56.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.991][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:56.993][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:56.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:56.995][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:56.997][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:56.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:56.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.002][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.003][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.005][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.007][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.012][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.014][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.016][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.018][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.023][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:57.024][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:57.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.026][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.028][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:57.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:57.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.033][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:57.034][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:57.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.036][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.038][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:57.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:57.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.043][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:57.045][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:57.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.047][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.048][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:57.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:57.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.053][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:57.055][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:57.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.057][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:57.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:57.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.064][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:57.065][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:57.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.067][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.069][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:57.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:57.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.074][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:57.075][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:57.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.078][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:57.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:57.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.084][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:57.086][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:57.087][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.088][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.090][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:57.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:57.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.095][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:57.096][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:57.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.099][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.100][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:57.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:57.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.105][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2024-05-04 16:07:57.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.110][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.115][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.120][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2024-05-04 16:07:57.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.125][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.130][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.135][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2024-05-04 16:07:57.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.140][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.145][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.150][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2024-05-04 16:07:57.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.155][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.160][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.165][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2024-05-04 16:07:57.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.170][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.175][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:57.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:57.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.194][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.200][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.210][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:57.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:57.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:57.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:57.239][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:57.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:57.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:57.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:57.246][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.247][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.249][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.256][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.257][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.259][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.262][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.267][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.268][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.270][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.272][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.277][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.279][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.281][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.283][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.288][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.289][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.291][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.293][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.298][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.300][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.302][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.304][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.309][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:57.310][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:57.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.312][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.314][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:57.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:57.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.319][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:57.320][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:57.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.323][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.324][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:57.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:57.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.329][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:57.331][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:57.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.333][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:57.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:57.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.340][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:57.341][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:57.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.343][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:57.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:57.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.350][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:57.351][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:57.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.354][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.355][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:57.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:57.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.361][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:57.362][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:57.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.364][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:57.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:57.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.371][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:57.372][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:57.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.375][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.376][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:57.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:57.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.381][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:57.383][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:57.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.385][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.387][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:57.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:57.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.392][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2024-05-04 16:07:57.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.397][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.402][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.407][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2024-05-04 16:07:57.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.412][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.417][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.422][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2024-05-04 16:07:57.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.427][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.431][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.436][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2024-05-04 16:07:57.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.441][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.446][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.451][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2024-05-04 16:07:57.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.456][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.461][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:57.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:57.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.471][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.476][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.487][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:57.507][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:57.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:57.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:57.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:57.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:57.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:57.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:57.525][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.526][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.528][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.535][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.536][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.539][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.540][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.545][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.547][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.549][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.551][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.556][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.557][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.559][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.561][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.572][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.574][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.576][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.578][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.583][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.584][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.586][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.588][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.594][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:57.595][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:57.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.597][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.599][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:57.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:57.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.604][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:57.605][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:57.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.607][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.609][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:57.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:57.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.614][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:57.615][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:57.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.618][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.619][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:57.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:57.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.624][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:57.626][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:57.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.628][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.629][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:57.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:57.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.634][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:57.636][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:57.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.638][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.639][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:57.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:57.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.645][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:57.646][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:57.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.649][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:57.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:57.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.655][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:57.657][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:57.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.659][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.660][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:57.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:57.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.666][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:57.667][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:57.668][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.669][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.671][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:57.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:57.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.676][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2024-05-04 16:07:57.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.681][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.686][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:57.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.691][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2024-05-04 16:07:57.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.696][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.701][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:57.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.706][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2024-05-04 16:07:57.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.711][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.716][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:57.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.721][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2024-05-04 16:07:57.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.726][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.731][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:57.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.736][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2024-05-04 16:07:57.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.741][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.746][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:57.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.751][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:57.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:57.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.756][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.760][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.770][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:57.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:57.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:57.835][self$createEntryFromContent] Accession numbers: 171341956, 171316324, 171316323.
biodb.DEBUG[2024-05-04 16:07:57.856][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 16:07:57.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:57.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:57.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:57.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:57.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:57.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:57.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:57.892][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.897][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.901][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:57.903][private$selectFields]
biodb.TRACE[2024-05-04 16:07:57.904][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:07:57.905][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:07:57.906][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:57.907][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.909][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.917][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.918][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.920][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.922][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.923][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:57.924][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:57.925][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.927][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.929][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.930][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2024-05-04 16:07:57.932][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.936][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.941][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.947][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [171341956].
biodb.DEBUG[2024-05-04 16:07:57.948][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:57.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:57.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:57.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:57.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:57.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:57.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:57.962][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.967][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.972][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:57.974][private$selectFields]
biodb.TRACE[2024-05-04 16:07:57.976][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:07:57.977][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:07:57.978][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:57.979][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.981][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.983][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.984][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.985][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.988][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.989][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:57.990][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:57.991][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.993][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:57.995][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:57.996][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2024-05-04 16:07:57.998][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:57.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.002][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.008][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.014][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [171316324].
biodb.DEBUG[2024-05-04 16:07:58.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:58.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:58.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:58.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:58.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:58.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:58.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:58.030][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.035][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.040][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:58.041][private$selectFields]
biodb.TRACE[2024-05-04 16:07:58.042][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:07:58.044][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:07:58.045][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:58.046][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.047][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.050][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.051][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.052][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.054][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.056][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:58.057][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:58.058][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.059][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.062][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.063][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2024-05-04 16:07:58.064][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.069][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.074][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.079][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [171316323].
biodb.DEBUG[2024-05-04 16:07:58.080][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 16:07:58.081][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-04 16:07:58.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:58.177][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:58.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:58.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:58.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:58.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:58.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:58.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:58.197][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.11358306:204.13358306[MonoisotopicMass]&retmax=3".
biodb.DEBUG[2024-05-04 16:07:58.200][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 16:07:58.202][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1279ae7853bbae0b1c59971aee79ce72".
biodb.TRACE[2024-05-04 16:07:58.204][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 16:07:58.216][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/1279ae7853bbae0b1c59971aee79ce72.content".
biodb.DEBUG[2024-05-04 16:07:58.218][private$loadEntries] Creating entries from ids [2]: "171338202, 171326566".
biodb.DEBUG[2024-05-04 16:07:58.220][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-04 16:07:58.222][cch$loadFileContent] Trying to load 2 files from cache: [2]: "171338202, 171326566".
biodb.TRACE[2024-05-04 16:07:58.223][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-05-04 16:07:58.247][loadFileContents] Loaded 2 files from cache: [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/171338202.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/171326566.xml".
biodb.DEBUG[2024-05-04 16:07:58.249][conn$getEntryContent] 2 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 16:07:58.250][self$createEntryFromContent] Creating PubChem Compound entries from 2 content(s).
biodb.DEBUG[2024-05-04 16:07:58.252][self$createEntryFromContent] Parsing 2 PubChem Compound entries.
biodb.DEBUG[2024-05-04 16:07:58.254][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:58.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:58.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:58.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:58.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:58.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:58.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:58.270][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.271][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.273][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.280][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.281][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.283][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.285][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.296][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.298][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.300][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.302][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.307][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.308][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.310][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.312][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.317][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.318][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.320][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.322][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.327][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.328][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.331][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.332][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.337][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:58.338][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.341][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.342][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:58.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.347][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:58.349][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:58.350][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.351][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.352][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:58.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:58.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.357][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:58.359][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:58.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.361][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:58.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:58.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.367][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:58.369][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:58.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.371][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:58.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:58.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.378][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:58.379][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:58.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.381][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.383][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:58.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:58.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.388][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:58.389][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:58.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.391][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:58.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:58.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.398][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:58.399][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:58.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.401][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.403][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:58.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:58.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.408][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:58.409][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:58.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.412][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.413][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:58.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:58.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.418][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2024-05-04 16:07:58.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.423][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.428][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.433][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2024-05-04 16:07:58.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.438][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.442][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.447][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2024-05-04 16:07:58.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.452][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.457][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.462][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2024-05-04 16:07:58.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.467][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.472][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.477][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2024-05-04 16:07:58.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.481][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.486][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:58.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:58.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.496][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.501][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.511][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:58.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:58.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:58.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:58.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:58.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:58.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:58.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:58.546][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.547][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.550][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.556][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.557][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.560][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.561][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.566][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.568][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.570][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.571][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.576][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.578][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.580][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.582][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.587][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.588][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.590][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.592][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.597][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.598][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.600][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.602][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.607][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:58.608][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.611][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.612][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:58.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:58.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.617][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:58.618][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:58.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.621][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.622][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:58.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:58.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.627][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:58.629][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:58.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.631][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.632][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:58.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:58.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.637][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:58.639][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:58.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.641][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.643][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:58.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:58.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.648][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:58.649][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:58.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.651][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.653][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:58.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:58.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.658][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:58.659][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:58.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.667][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:58.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:58.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.674][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:58.675][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:58.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.678][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.679][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:58.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:58.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.684][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:58.685][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:58.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.688][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.689][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:58.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:58.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.694][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2024-05-04 16:07:58.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.699][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.704][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:58.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.709][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2024-05-04 16:07:58.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.714][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.718][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:58.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.723][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2024-05-04 16:07:58.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.728][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.733][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:58.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.738][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2024-05-04 16:07:58.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.743][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.748][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:58.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.752][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2024-05-04 16:07:58.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.758][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.762][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:58.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:58.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:58.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.772][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.777][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.787][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:58.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:58.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:58.836][self$createEntryFromContent] Accession numbers: 171338202, 171326566.
biodb.DEBUG[2024-05-04 16:07:58.837][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 16:07:58.839][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:58.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:58.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:58.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:58.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:58.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:58.852][FUN] Functions in observer BiodbConfig: [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[2024-05-04 16:07:58.863][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.868][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.890][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:58.891][private$selectFields]
biodb.TRACE[2024-05-04 16:07:58.892][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:07:58.893][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:07:58.895][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:58.896][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.897][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.899][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.901][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.902][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.904][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.905][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:58.915][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:58.916][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.917][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.919][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.921][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2024-05-04 16:07:58.922][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.927][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.932][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.937][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [171364948].
biodb.DEBUG[2024-05-04 16:07:58.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:58.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:58.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:58.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:58.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:58.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:58.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:58.953][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.957][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.962][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:58.963][private$selectFields]
biodb.TRACE[2024-05-04 16:07:58.964][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:07:58.966][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:07:58.967][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:58.968][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.969][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.972][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.973][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.975][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.978][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.980][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:58.981][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:58.982][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.983][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.986][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.987][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2024-05-04 16:07:58.988][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.993][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:58.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:58.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:58.998][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.009][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [171338202].
biodb.DEBUG[2024-05-04 16:07:59.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:59.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:59.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:59.020][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:59.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:59.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:59.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:59.025][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.030][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.035][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:59.036][private$selectFields]
biodb.TRACE[2024-05-04 16:07:59.037][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:07:59.038][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:07:59.039][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:59.041][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.042][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.044][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.046][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.047][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.049][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.050][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:59.052][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:07:59.053][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.054][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.055][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.056][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.058][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2024-05-04 16:07:59.059][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.064][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.069][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.074][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [171326566].
biodb.DEBUG[2024-05-04 16:07:59.075][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 16:07:59.076][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.DEBUG[2024-05-04 16:07:59.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:59.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:59.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:59.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:59.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:59.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:59.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:59.098][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.04897142:226.06897142[MonoisotopicMass]&retmax=3".
biodb.DEBUG[2024-05-04 16:07:59.102][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 16:07:59.104][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 16:07:59.105][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.04897142%3A226.06897142%5BMonoisotopicMass%5D&retmax=3".
biodb.TRACE[2024-05-04 16:07:59.168][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.04897142%3A226.06897142%5BMonoisotopicMass%5D&retmax=3 does not exist.
biodb.TRACE[2024-05-04 16:07:59.169][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 16:07:59.171][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.04897142%3A226.06897142%5BMonoisotopicMass%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 16:07:59.173][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.04897142%3A226.06897142%5BMonoisotopicMass%5D&retmax=3).
biodb.DEBUG[2024-05-04 16:07:59.274][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 16:07:59.279][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/6eb047352a5797ace7dc0cd8f5af7cbf.content"
biodb.INFO [2024-05-04 16:07:59.312][biodb::testThat]
biodb.INFO [2024-05-04 16:07:59.314][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-04 16:07:59.315][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:59.316][biodb::testThat]
biodb.TRACE[2024-05-04 16:07:59.320][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 16:07:59.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 16:07:59.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.325][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 16:07:59.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 16:07:59.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:59.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:59.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:59.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:59.381][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:59.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:59.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:59.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:59.392][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[2024-05-04 16:07:59.396][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 16:07:59.397][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aa9cb23a1eb4b2596e7c242b1c35f744".
biodb.TRACE[2024-05-04 16:07:59.399][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 16:07:59.409][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/aa9cb23a1eb4b2596e7c242b1c35f744.content".
biodb.DEBUG[2024-05-04 16:07:59.412][private$loadEntries] Creating entries from ids [2]: "171326496, 171236632".
biodb.DEBUG[2024-05-04 16:07:59.414][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-04 16:07:59.416][cch$loadFileContent] Trying to load 2 files from cache: [2]: "171326496, 171236632".
biodb.TRACE[2024-05-04 16:07:59.418][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-05-04 16:07:59.442][loadFileContents] Loaded 2 files from cache: [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/171326496.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/171236632.xml".
biodb.DEBUG[2024-05-04 16:07:59.444][conn$getEntryContent] 2 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 16:07:59.446][self$createEntryFromContent] Creating PubChem Compound entries from 2 content(s).
biodb.DEBUG[2024-05-04 16:07:59.447][self$createEntryFromContent] Parsing 2 PubChem Compound entries.
biodb.DEBUG[2024-05-04 16:07:59.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:59.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:59.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:59.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:59.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:59.461][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:59.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:59.465][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:59.466][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:59.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.469][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:59.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:59.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.476][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:59.477][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:59.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.479][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.481][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:59.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:59.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.486][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:59.487][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:59.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.490][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.491][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:59.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:59.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.496][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:59.498][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:59.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.500][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.502][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:59.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:59.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.507][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:59.508][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:59.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.510][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.512][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:59.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:59.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.517][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:59.518][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:59.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.521][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.522][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:59.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:59.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.527][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:59.529][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:59.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.531][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.533][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:59.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:59.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.538][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:59.539][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:59.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.541][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.543][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:07:59.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:07:59.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.548][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:59.549][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:59.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.553][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.554][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:07:59.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:07:59.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.560][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:59.561][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:59.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.564][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:07:59.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:07:59.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.570][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:59.572][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:59.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.574][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.576][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:07:59.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:07:59.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.778][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:59.779][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.781][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:07:59.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:07:59.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.788][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:59.789][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:59.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.791][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.793][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:59.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:07:59.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.798][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:59.799][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:59.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.801][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.803][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:59.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:07:59.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.808][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2024-05-04 16:07:59.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:59.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.812][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:59.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:59.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.817][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:59.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:59.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.822][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2024-05-04 16:07:59.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:59.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.827][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:59.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:59.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.832][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:59.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:59.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.836][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2024-05-04 16:07:59.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:59.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.841][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:59.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:59.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.846][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:59.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:59.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.851][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2024-05-04 16:07:59.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:59.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.855][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:59.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:59.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.860][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:59.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:59.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.865][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2024-05-04 16:07:59.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:59.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.870][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:59.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:59.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.874][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:59.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:59.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.879][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:59.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:59.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.884][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.889][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:59.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:59.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.898][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:07:59.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:59.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:59.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:59.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:59.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:59.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:59.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:59.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:59.919][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:59.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:59.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:59.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:59.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:59.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:59.934][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:59.935][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:59.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.937][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:59.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:59.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.944][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:59.945][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:59.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.947][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.949][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:59.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:07:59.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.954][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:59.955][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:59.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.957][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.959][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:59.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:07:59.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.964][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:59.965][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:59.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.967][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.969][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:59.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:07:59.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.974][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:59.976][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:59.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.978][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.980][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:59.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:07:59.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.984][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:59.986][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:59.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.988][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.989][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:59.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:07:59.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.994][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:07:59.996][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:07:59.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:59.998][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:59.999][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-04 16:08:00.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:00.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.004][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:00.006][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:00.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.008][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.009][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:00.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:00.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.014][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:00.015][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:00.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.018][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:00.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:00.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.024][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:00.025][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:00.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.028][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:00.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:00.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.034][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:00.035][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:00.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.037][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.039][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:00.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:00.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.044][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:08:00.045][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.047][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2024-05-04 16:08:00.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.054][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:00.055][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:00.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.057][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.059][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:00.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:00.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.064][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:00.065][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:00.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.067][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.069][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:00.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:00.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.074][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2024-05-04 16:08:00.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:00.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.078][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:00.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:00.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.083][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:00.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:00.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.088][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2024-05-04 16:08:00.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:00.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.093][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:00.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:00.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.098][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:00.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:00.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.102][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2024-05-04 16:08:00.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:00.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.107][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:00.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:00.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.112][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:00.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:00.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.117][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2024-05-04 16:08:00.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:00.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.121][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:00.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:00.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.126][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:00.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:00.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.131][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2024-05-04 16:08:00.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:00.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.136][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:00.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:00.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.141][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:00.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:00.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:00.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:00.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.156][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.160][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:00.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:00.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.170][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:00.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:00.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:00.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:00.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:00.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:00.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:00.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:00.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:00.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:00.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:00.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:00.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:00.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:00.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:00.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:00.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:00.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:00.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:08:00.217][self$createEntryFromContent] Accession numbers: 171326496, 171236632.
biodb.DEBUG[2024-05-04 16:08:00.218][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 16:08:00.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:00.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:00.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:00.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:00.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:00.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:00.238][FUN] Functions in observer BiodbConfig: [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[2024-05-04 16:08:00.241][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.248][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.254][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.256][private$selectFields]
biodb.TRACE[2024-05-04 16:08:00.258][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:08:00.259][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:08:00.261][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.263][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.265][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.268][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.270][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.271][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.273][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.274][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.276][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.277][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.278][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.280][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.281][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2024-05-04 16:08:00.283][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.287][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.292][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.297][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [171326497].
biodb.DEBUG[2024-05-04 16:08:00.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:00.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:00.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:00.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:00.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:00.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:00.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:08:00.313][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.317][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.322][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.323][private$selectFields]
biodb.TRACE[2024-05-04 16:08:00.324][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:08:00.325][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:08:00.326][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.328][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.329][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.331][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.332][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.334][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.336][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.337][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.338][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.339][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.341][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.343][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.344][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2024-05-04 16:08:00.345][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.350][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.355][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.360][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [171326496].
biodb.DEBUG[2024-05-04 16:08:00.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:00.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:00.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:00.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:00.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:00.372][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:00.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:08:00.375][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.380][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.384][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.386][private$selectFields]
biodb.TRACE[2024-05-04 16:08:00.387][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:08:00.388][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:08:00.389][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.390][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.391][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.394][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.395][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.396][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.398][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.400][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.401][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.402][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.403][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.406][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.407][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2024-05-04 16:08:00.408][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.413][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.418][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.423][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [171236632].
biodb.DEBUG[2024-05-04 16:08:00.424][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 16:08:00.426][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.DEBUG[2024-05-04 16:08:00.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:00.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:00.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:00.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:00.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:00.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:00.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:00.448][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[2024-05-04 16:08:00.452][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 16:08:00.453][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 16:08:00.455][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2024-05-04 16:08:00.502][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2024-05-04 16:08:00.503][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 16:08:00.505][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 16:08:00.507][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=226.18660715%3A226.19339285%5BMolecularWeight%5D&retmax=3).
biodb.DEBUG[2024-05-04 16:08:00.550][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 16:08:00.553][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/cdac68f12e8f2043e94276de0cd65925.content"
biodb.INFO [2024-05-04 16:08:00.586][biodb::testThat]
biodb.INFO [2024-05-04 16:08:00.587][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-04 16:08:00.588][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:08:00.590][biodb::testThat]
biodb.TRACE[2024-05-04 16:08:00.594][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 16:08:00.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 16:08:00.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.598][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 16:08:00.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 16:08:00.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:08:00.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:00.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:00.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:00.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:00.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:00.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:00.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:00.670][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[2024-05-04 16:08:00.674][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 16:08:00.675][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2616ca37a6f6e1bc281f8c51bc53ce81".
biodb.TRACE[2024-05-04 16:08:00.677][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 16:08:00.679][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/2616ca37a6f6e1bc281f8c51bc53ce81.content".
biodb.DEBUG[2024-05-04 16:08:00.681][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 16:08:00.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:00.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:00.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:00.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:00.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:00.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:00.695][FUN] Functions in observer BiodbConfig: [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[2024-05-04 16:08:00.697][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.701][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.706][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.707][private$selectFields]
biodb.TRACE[2024-05-04 16:08:00.708][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:08:00.709][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:08:00.710][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.712][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.713][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.715][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.716][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.718][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.720][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.721][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.722][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.723][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.725][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.727][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.728][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2024-05-04 16:08:00.729][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.734][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.739][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.744][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [171364948].
biodb.DEBUG[2024-05-04 16:08:00.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:00.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:00.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:00.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:00.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:00.756][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:00.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:08:00.759][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.764][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.768][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.769][private$selectFields]
biodb.TRACE[2024-05-04 16:08:00.771][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:08:00.772][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:08:00.773][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.774][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.775][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.778][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.779][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.780][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.782][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.783][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.785][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.786][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.787][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.789][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.790][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2024-05-04 16:08:00.792][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.796][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.801][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.806][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [171334113].
biodb.DEBUG[2024-05-04 16:08:00.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:00.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:00.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:00.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:00.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:00.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:00.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:08:00.821][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.826][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.831][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.832][private$selectFields]
biodb.TRACE[2024-05-04 16:08:00.833][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:08:00.834][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:08:00.835][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.836][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.838][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.840][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.841][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.842][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.845][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.846][private$selectFields] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.847][private$organizeFieldsByGroups] Fields [1]: "ncbi.pubchem.comp.id"
biodb.TRACE[2024-05-04 16:08:00.848][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.849][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.852][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.853][private$organizeFieldsByGroups] Groups [2]: "ncbi.pubchem.comp.id, list()"
biodb.TRACE[2024-05-04 16:08:00.854][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.859][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.864][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:00.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.869][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [ncbi.pubchem.comp.id] [171326497].
biodb.DEBUG[2024-05-04 16:08:00.870][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 16:08:00.871][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.DEBUG[2024-05-04 16:08:00.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:00.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:00.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:00.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:00.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:00.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:00.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:00.893][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[2024-05-04 16:08:00.896][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 16:08:00.898][cch$loadFileContent] Trying to load 1 files from cache: [1]: "69c19f6998e271aebdcd09a030d9b450".
biodb.TRACE[2024-05-04 16:08:00.899][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 16:08:00.901][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/69c19f6998e271aebdcd09a030d9b450.content".
biodb.TRACE[2024-05-04 16:08:00.918][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:00.920][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:00.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.922][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.923][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.924][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.927][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 16:08:00.929][biodb::testThat]
biodb.INFO [2024-05-04 16:08:00.930][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2024-05-04 16:08:00.931][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:08:00.932][biodb::testThat]
biodb.TRACE[2024-05-04 16:08:00.936][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 16:08:00.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 16:08:00.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.941][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 16:08:00.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 16:08:00.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:00.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:00.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:00.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:08:00.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:00.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:00.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:01.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:01.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:01.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:01.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:01.012][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[2024-05-04 16:08:01.016][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 16:08:01.017][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 16:08:01.019][private$doSendRequestOnce] Sent URL is "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3".
biodb.TRACE[2024-05-04 16:08:01.077][doesRCurlRequestUrlExist] According to RCurl, URL https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3 does not exist.
biodb.TRACE[2024-05-04 16:08:01.078][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-05-04 16:08:01.080][getUrlRequestResult] URL "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-05-04 16:08:01.082][getBaseUrlRequestResult] Using base::url() for sending request (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=204.03%3A204.25%5BMolecularWeight%5D&retmax=3).
biodb.DEBUG[2024-05-04 16:08:01.248][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 16:08:01.251][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/9701d2e1a6b096cdfd56943877648611.content"
biodb.INFO [2024-05-04 16:08:01.283][biodb::testThat]
biodb.INFO [2024-05-04 16:08:01.284][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2024-05-04 16:08:01.285][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:08:01.287][biodb::testThat]
biodb.TRACE[2024-05-04 16:08:01.290][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 16:08:01.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 16:08:01.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.295][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 16:08:01.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 16:08:01.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.314][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:08:01.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:01.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:01.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:01.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:01.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:01.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:01.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:01.359][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[2024-05-04 16:08:01.363][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 16:08:01.364][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2616ca37a6f6e1bc281f8c51bc53ce81".
biodb.TRACE[2024-05-04 16:08:01.366][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 16:08:01.368][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/2616ca37a6f6e1bc281f8c51bc53ce81.content".
biodb.DEBUG[2024-05-04 16:08:01.370][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 16:08:01.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:01.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:01.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:01.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:01.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:01.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:01.384][FUN] Functions in observer BiodbConfig: [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[2024-05-04 16:08:01.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:01.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:01.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:01.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:01.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.394][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.399][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.404][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.409][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.413][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.418][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.423][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.428][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.432][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.437][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.442][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:01.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:01.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.446][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:01.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:01.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.451][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:01.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:01.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.456][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:01.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:01.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.460][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.465][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.470][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:01.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:01.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.474][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:01.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:01.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:01.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:01.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.503][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:01.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:01.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.507][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.512][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.517][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.522][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.526][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:01.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:01.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.531][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:01.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:01.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.536][private$selectFields] Fields [16]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2024-05-04 16:08:01.537][private$selectFields]
biodb.TRACE[2024-05-04 16:08:01.538][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:08:01.539][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:08:01.540][private$selectFields] Fields [16]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2024-05-04 16:08:01.541][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:01.543][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:01.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.545][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.546][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.547][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.550][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.551][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.552][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.555][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.557][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.558][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.560][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.562][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.563][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.565][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.566][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.568][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.570][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.571][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:01.573][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:01.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.575][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.576][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:01.578][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:01.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.580][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.581][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.588][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.590][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.591][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:01.593][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:01.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.595][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.596][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.597][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.599][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.601][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.602][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.604][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.605][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:01.606][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:01.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.609][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.610][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.611][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.613][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.614][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.616][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.618][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.619][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:01.620][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:01.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.622][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.624][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:01.625][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:01.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.627][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.628][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.629][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.632][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.633][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.634][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.636][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.637][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.639][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.641][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.642][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.643][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.645][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.647][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.648][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.649][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.650][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.651][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:01.653][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:01.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.655][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.656][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:01.657][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:01.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.659][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.660][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.662][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.663][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.664][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.665][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:01.666][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:01.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.669][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.670][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.671][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.673][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.674][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.676][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.678][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.679][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:01.680][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:01.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.682][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.684][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.685][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.687][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.688][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.689][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.692][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.693][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:01.694][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:01.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.696][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.697][private$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[2024-05-04 16:08:01.699][private$organizeFieldsByGroups] Fields [16]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2024-05-04 16:08:01.700][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:01.701][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:01.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.703][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.704][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.706][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.708][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.709][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.710][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.712][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.714][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.715][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.717][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.718][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.719][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.722][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.723][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.724][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.726][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.727][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:01.729][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:01.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.731][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.732][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:01.733][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:01.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.735][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.737][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.738][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.740][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.741][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:01.742][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:01.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.745][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.746][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.747][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.749][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.750][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.752][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.754][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.755][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:01.756][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:01.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.758][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.759][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.761][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.763][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.764][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.765][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.768][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.769][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:01.770][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:01.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.772][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.773][private$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[2024-05-04 16:08:01.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:01.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:01.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:01.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:01.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:01.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:01.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.789][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.794][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.798][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:01.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.803][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.808][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.812][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:01.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.817][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.822][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.827][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:01.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.831][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.836][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.841][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:01.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.846][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.850][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.855][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:01.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.860][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:01.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:01.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.865][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:01.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:01.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.870][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:01.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:01.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.874][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:01.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:01.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.879][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:01.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:01.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.884][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:01.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:01.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.889][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.898][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:01.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.903][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:01.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:01.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.908][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:01.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:01.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.912][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:01.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:01.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:01.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:01.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:01.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:01.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:01.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:01.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:01.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:01.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.967][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.972][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.976][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:01.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.981][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.986][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.991][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:01.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:01.996][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:01.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:01.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:01.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.000][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.005][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.018][private$entriesToListOfDataframes] Entry converted to data frame: [1, 16]: [accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, ...] [171364948, (2S)-2-amino-6-guanidino-6-hydroxy-hexanoic acid, (2S)-2-amino-6-(diaminomethylideneamino)-6-hydroxyhexanoic acid, (2S)-2-amino-6-(diaminomethylideneamino)-6-hydroxyhexanoic acid, (2S)-2-azanyl-6-[bis(azanyl)methylideneamino]-6-oxidanyl-hexanoic acid, ...].
biodb.DEBUG[2024-05-04 16:08:02.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:02.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:02.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:02.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:02.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:02.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:02.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:08:02.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:02.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:02.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:02.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:02.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.043][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.047][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.052][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.057][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.062][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.066][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.071][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.076][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.080][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.085][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.090][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:02.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:02.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.094][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:02.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:02.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.099][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:02.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:02.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:02.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:02.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.109][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.113][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.118][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:02.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:02.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.123][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:02.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:02.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:02.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:02.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:02.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:02.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.156][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.160][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.165][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.170][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.175][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.179][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.184][private$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[2024-05-04 16:08:02.185][private$selectFields]
biodb.TRACE[2024-05-04 16:08:02.186][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:08:02.187][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:08:02.189][private$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[2024-05-04 16:08:02.190][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:02.191][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:02.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.193][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.194][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.196][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.198][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.199][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.200][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.203][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.204][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.205][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.207][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.208][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.210][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.212][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.213][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.214][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.217][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.218][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:02.219][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:02.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.221][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.223][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:02.224][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:02.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.226][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.227][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.229][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.231][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.232][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:02.233][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:02.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.236][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.237][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.238][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.240][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.241][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.243][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.245][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.246][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:02.247][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:02.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.250][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.251][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.252][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.254][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.255][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.257][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.259][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.260][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.261][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.263][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.265][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:02.266][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:02.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.268][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.269][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.271][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.273][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.274][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.275][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.278][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.279][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.280][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.282][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.284][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.285][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.287][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.288][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.290][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.292][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.293][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:02.294][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:02.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.302][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.303][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:02.304][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:02.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.307][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.308][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.309][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.311][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.312][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:02.314][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:02.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.316][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.317][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.318][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.320][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.321][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.323][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.325][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.326][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:02.327][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:02.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.330][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.331][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.332][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.334][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.335][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.336][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.339][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.340][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.341][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.343][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.344][private$selectFields] Fields [16]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2024-05-04 16:08:02.346][private$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[2024-05-04 16:08:02.347][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:02.348][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:02.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.350][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.351][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.353][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.355][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.356][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.357][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.358][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.360][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.361][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.362][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.364][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.365][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.366][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.369][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.370][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.371][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.373][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.375][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:02.376][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:02.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.378][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.379][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:02.380][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:02.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.383][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.384][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.385][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.387][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.388][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:02.390][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:02.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.392][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.393][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.394][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.396][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.397][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.399][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.401][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.402][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:02.403][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:02.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.405][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.407][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.408][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.410][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.411][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.413][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.415][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.416][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.417][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.419][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.421][private$organizeFieldsByGroups] Groups [2]: "c("accession", "comp.iupac.name.allowed", "comp.iupac.name.cas", "comp.iupac.name.pref", "comp.iupac.name.syst", "comp.iupac.name.trad", "formula", "inchi", "inchikey", "logp", "molecular.mass", "monoisotopic.mass", "name", "ncbi.pubchem.comp.id", "smiles.canonical", "smiles.isomeric"), list()"
biodb.TRACE[2024-05-04 16:08:02.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:02.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:02.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:02.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:02.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:02.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:02.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.436][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.441][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.445][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.450][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.455][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.460][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.464][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.469][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.474][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.479][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.483][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.488][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.493][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.502][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.507][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:02.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:02.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.512][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:02.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:02.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.517][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:02.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:02.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.523][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:02.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:02.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.527][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:02.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:02.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.532][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:02.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:02.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.546][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.551][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:02.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:02.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.556][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:02.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:02.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.560][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:02.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:02.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.594][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:02.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:02.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.599][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:02.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:02.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.603][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:02.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:02.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.608][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.613][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.618][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.623][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.627][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.632][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.637][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.642][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.647][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.663][private$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, ...] [171334113, 4-pyrazolo[1,5-a]pyrazin-4-ylmorpholine, 4-(4-pyrazolo[1,5-a]pyrazinyl)morpholine, 4-pyrazolo[1,5-a]pyrazin-4-ylmorpholine, 4-pyrazolo[1,5-a]pyrazin-4-ylmorpholine, ...].
biodb.DEBUG[2024-05-04 16:08:02.664][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:02.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:02.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:02.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:02.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:02.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:02.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:08:02.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:02.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:02.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:02.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:02.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.688][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.692][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.697][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.702][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.706][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.711][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.716][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.720][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.725][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.730][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.735][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:02.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:02.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.739][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:02.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:02.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.744][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:02.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:02.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:02.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:02.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.763][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:02.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:02.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.768][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:02.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:02.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:02.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:02.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:02.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:02.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.800][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.805][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.810][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.815][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.819][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.824][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.829][private$selectFields] Fields [16]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2024-05-04 16:08:02.830][private$selectFields]
biodb.TRACE[2024-05-04 16:08:02.831][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 16:08:02.832][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 16:08:02.833][private$selectFields] Fields [16]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2024-05-04 16:08:02.834][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:02.836][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:02.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.838][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.839][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.840][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.843][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.844][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.845][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.847][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.849][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.850][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.852][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.853][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.854][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.856][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.857][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.858][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.859][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.861][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.863][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:02.864][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:02.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.866][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.867][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:02.868][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:02.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.871][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.872][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.873][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.875][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.876][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:02.878][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:02.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.880][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.881][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.882][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.884][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.886][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.887][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.889][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.890][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:02.891][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:02.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.894][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.895][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.896][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.898][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.899][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.901][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.903][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.904][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.905][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.907][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.909][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:02.910][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:02.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.912][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.913][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.915][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.917][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.918][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.919][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.921][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.923][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.924][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:02.925][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.926][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.927][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.929][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:02.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.931][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.932][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.933][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:02.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.936][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.937][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:02.938][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:02.939][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.940][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.941][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:02.943][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:02.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.945][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.946][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.947][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:02.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.949][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.951][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:02.952][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:02.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.954][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.955][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.957][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:02.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.959][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.960][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.961][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:02.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.963][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.965][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:02.966][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:02.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.969][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.970][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.972][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:02.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.974][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.975][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.976][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:02.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.979][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.980][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.981][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:02.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.984][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.985][private$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[2024-05-04 16:08:02.986][private$organizeFieldsByGroups] Fields [16]: "accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, comp.iupac.name.trad, formula, inchi, inchikey, logp, ..."
biodb.TRACE[2024-05-04 16:08:02.987][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:02.989][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:02.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.991][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.992][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.993][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:02.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:02.996][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:02.997][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.998][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:02.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.001][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.002][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:03.003][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:03.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.005][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.007][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:03.008][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:03.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.015][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.016][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:03.018][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:03.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.020][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.021][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:03.022][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:03.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.024][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.026][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:03.027][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:03.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.029][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.030][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:03.031][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:03.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.034][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.035][ef$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:03.036][ef$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:03.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.038][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.039][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:03.041][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:03.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.043][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.044][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:03.045][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:03.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.048][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.049][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:03.050][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:03.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.052][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.053][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:03.055][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:03.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.057][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.058][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:03.059][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:03.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.061][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.063][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:03.064][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:03.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.066][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.067][private$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[2024-05-04 16:08:03.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:03.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:03.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:03.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:03.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:03.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:03.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.083][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:03.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:03.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.088][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:03.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:03.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.092][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:03.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2024-05-04 16:08:03.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.097][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:03.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:03.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.102][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:03.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:03.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.107][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:03.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2024-05-04 16:08:03.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.112][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:03.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:03.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.116][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:03.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:03.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.121][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:03.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2024-05-04 16:08:03.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.126][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:03.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:03.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.132][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:03.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:03.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.137][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:03.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-04 16:08:03.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.142][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:03.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:03.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.147][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:03.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:03.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.151][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:03.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-04 16:08:03.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.156][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:03.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:03.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.161][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:03.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:03.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.166][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:08:03.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:08:03.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:03.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:03.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.175][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:03.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:03.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.180][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:08:03.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:08:03.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.185][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:03.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:03.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.190][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:03.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:03.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.195][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:08:03.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:08:03.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.200][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:03.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:03.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.206][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:03.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:03.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.214][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2024-05-04 16:08:03.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2024-05-04 16:08:03.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.220][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:03.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:03.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:03.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:03.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:03.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:08:03.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:03.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:03.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:03.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:03.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:03.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 16:08:03.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.249][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:03.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:03.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:03.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:03.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:08:03.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:08:03.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.263][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:03.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:03.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.268][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:03.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:03.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.273][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:03.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:03.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.278][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:03.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:03.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.282][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:03.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:03.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.287][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:03.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2024-05-04 16:08:03.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.292][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:03.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:03.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.297][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:03.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:03.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.302][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:03.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2024-05-04 16:08:03.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:03.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:03.314][private$entriesToListOfDataframes] Entry converted to data frame: [1, 16]: [accession, comp.iupac.name.allowed, comp.iupac.name.cas, comp.iupac.name.pref, comp.iupac.name.syst, ...] [171326497, 5-[[3-(difluoromethyl)azetidin-1-yl]methyl]thiazole, 5-[[3-(difluoromethyl)-1-azetidinyl]methyl]thiazole, 5-[[3-(difluoromethyl)azetidin-1-yl]methyl]-1,3-thiazole, 5-[[3-[bis(fluoranyl)methyl]azetidin-1-yl]methyl]-1,3-thiazole, ...].
biodb.DEBUG[2024-05-04 16:08:03.315][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 16:08:03.316][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.DEBUG[2024-05-04 16:08:03.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:03.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.339][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[2024-05-04 16:08:03.342][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 16:08:03.344][cch$loadFileContent] Trying to load 1 files from cache: [1]: "69c19f6998e271aebdcd09a030d9b450".
biodb.TRACE[2024-05-04 16:08:03.346][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 16:08:03.348][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75/69c19f6998e271aebdcd09a030d9b450.content".
biodb.INFO [2024-05-04 16:08:03.365][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-04 16:08:03.367][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.pubchem.comp from the request scheduler
biodb.INFO [2024-05-04 16:08:03.368][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2024-05-04 16:08:03.369][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-04 16:08:03.370][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.373][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.380][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-04 16:08:03.386][biodb::testContext]
biodb.INFO [2024-05-04 16:08:03.387][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:08:03.388][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2024-05-04 16:08:03.390][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:08:03.391][biodb::testContext]
biodb.INFO [2024-05-04 16:08:03.393][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:08:03.396][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-04 16:08:03.401][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:08:03.402][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-04 16:08:03.404][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-04 16:08:03.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.408][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-04 16:08:03.409][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-04 16:08:03.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.414][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-04 16:08:03.415][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-04 16:08:03.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.419][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-04 16:08:03.421][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-04 16:08:03.422][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-04 16:08:03.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.426][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-04 16:08:03.427][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-04 16:08:03.429][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-04 16:08:03.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.433][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-04 16:08:03.434][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-04 16:08:03.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.439][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-04 16:08:03.440][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-04 16:08:03.441][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-04 16:08:03.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.445][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-04 16:08:03.447][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-04 16:08:03.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.451][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-04 16:08:03.452][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-04 16:08:03.453][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-04 16:08:03.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.458][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:08:03.459][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-04 16:08:03.460][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-04 16:08:03.461][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-04 16:08:03.463][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-04 16:08:03.464][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-04 16:08:03.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.468][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-04 16:08:03.470][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-04 16:08:03.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.474][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-04 16:08:03.475][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-04 16:08:03.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.478][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[2024-05-04 16:08:03.480][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-04 16:08:03.481][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-04 16:08:03.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.485][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-04 16:08:03.486][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-04 16:08:03.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.490][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[2024-05-04 16:08:03.491][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-04 16:08:03.492][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-04 16:08:03.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.496][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:08:03.498][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-04 16:08:03.501][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-04 16:08:03.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.506][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-04 16:08:03.507][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-04 16:08:03.508][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-04 16:08:03.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.513][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-04 16:08:03.515][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:03.516][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-04 16:08:03.517][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.518][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:08:03.520][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.521][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:08:03.522][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:03.523][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:08:03.524][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:08:03.525][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:08:03.527][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.528][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-04 16:08:03.529][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:08:03.530][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:03.531][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.532][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:08:03.532][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:08:03.532][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:08:03.532][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:08:03.532][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:08:03.534][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:08:03.535][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:03.536][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:03.537][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:08:03.538][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:03.539][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:03.540][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:08:03.542][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:03.543][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:08:03.544][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:08:03.545][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:03.546][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:03.548][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-04 16:08:03.549][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:03.551][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:08:03.552][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.553][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:08:03.554][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.555][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:08:03.557][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:03.558][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:08:03.559][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:08:03.560][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:08:03.561][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.562][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-04 16:08:03.564][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:08:03.565][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:03.566][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.567][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:08:03.567][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:08:03.567][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:08:03.567][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:08:03.567][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:08:03.569][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:08:03.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:03.571][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:03.572][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:08:03.573][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:03.574][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:03.575][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:08:03.576][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:03.578][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:08:03.579][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:08:03.580][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:03.581][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:03.582][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-04 16:08:03.584][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.585][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-04 16:08:03.587][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.588][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:08:03.589][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.590][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:08:03.591][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:03.593][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:08:03.594][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:08:03.595][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:08:03.596][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:03.597][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-04 16:08:03.598][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:08:03.600][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:03.601][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.602][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:03.603][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:08:03.604][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:03.605][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:03.607][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:08:03.608][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:03.609][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:03.610][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:08:03.611][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:03.612][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:08:03.613][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:08:03.614][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:03.616][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:03.617][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-04 16:08:03.619][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.620][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:08:03.621][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.622][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:08:03.624][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.625][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:08:03.626][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:03.627][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:08:03.628][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:08:03.630][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:08:03.631][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:03.632][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-04 16:08:03.633][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:08:03.634][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:03.635][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:03.637][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:03.638][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:08:03.639][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:03.640][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:03.641][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:08:03.643][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:03.644][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:03.645][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:08:03.646][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:03.647][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:08:03.648][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:08:03.649][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:03.651][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:03.652][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:08:03.653][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.654][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[2024-05-04 16:08:03.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.660][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[2024-05-04 16:08:03.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.682][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.DEBUG[2024-05-04 16:08:03.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.716][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[2024-05-04 16:08:03.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.733][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[2024-05-04 16:08:03.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.756][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-04 16:08:03.758][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-04 16:08:03.760][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-04 16:08:03.761][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-04 16:08:03.763][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 16:08:03.764][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-04 16:08:03.766][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-04 16:08:03.767][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-04 16:08:03.769][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 16:08:03.770][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-04 16:08:03.772][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 16:08:03.773][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-04 16:08:03.775][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-04 16:08:03.776][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-04 16:08:03.778][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 16:08:03.779][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 16:08:03.781][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-04 16:08:03.782][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-04 16:08:03.784][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 16:08:03.786][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-04 16:08:03.787][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-04 16:08:03.789][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-04 16:08:03.790][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-04 16:08:03.792][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-04 16:08:03.793][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-04 16:08:03.795][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-04 16:08:03.796][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-04 16:08:03.798][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-04 16:08:03.799][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-04 16:08:03.801][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-04 16:08:03.802][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-04 16:08:03.804][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-04 16:08:03.806][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-04 16:08:03.807][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-04 16:08:03.809][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-04 16:08:03.810][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-04 16:08:03.812][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-04 16:08:03.813][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-04 16:08:03.815][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-04 16:08:03.816][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-04 16:08:03.818][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-04 16:08:03.819][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-04 16:08:03.821][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-04 16:08:03.822][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-04 16:08:03.824][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-04 16:08:03.825][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 16:08:03.827][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-04 16:08:03.829][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-04 16:08:03.830][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-04 16:08:03.832][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-04 16:08:03.833][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-04 16:08:03.835][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-04 16:08:03.836][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-04 16:08:03.838][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-04 16:08:03.839][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-04 16:08:03.841][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-04 16:08:03.842][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-04 16:08:03.844][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-04 16:08:03.845][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-04 16:08:03.847][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-04 16:08:03.848][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-04 16:08:03.850][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-04 16:08:03.852][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-04 16:08:03.853][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-04 16:08:03.855][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-04 16:08:03.856][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-04 16:08:03.858][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 16:08:03.859][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 16:08:03.861][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-04 16:08:03.862][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-04 16:08:03.864][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-04 16:08:03.865][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-04 16:08:03.867][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-04 16:08:03.868][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-04 16:08:03.870][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-04 16:08:03.871][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-04 16:08:03.873][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-04 16:08:03.874][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-04 16:08:03.876][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-04 16:08:03.878][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-04 16:08:03.879][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-04 16:08:03.881][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-04 16:08:03.882][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-04 16:08:03.884][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-04 16:08:03.886][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:08:03.887][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:08:03.888][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.891][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.892][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[2024-05-04 16:08:03.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.899][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[2024-05-04 16:08:03.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.907][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[2024-05-04 16:08:03.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.914][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[2024-05-04 16:08:03.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.937][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[2024-05-04 16:08:03.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.959][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[2024-05-04 16:08:03.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:03.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:03.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:03.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:03.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:03.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:03.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:03.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:04.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:04.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:04.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:04.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:04.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:04.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:04.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:04.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:04.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:04.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:04.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:04.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:04.013][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[2024-05-04 16:08:04.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:08:04.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:04.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:04.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:04.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:04.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:04.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:08:04.024][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2024-05-04 16:08:04.027][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2024-05-04 16:08:04.029][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.030][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2024-05-04 16:08:04.031][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.032][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:08:04.033][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.035][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:08:04.036][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.037][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:08:04.038][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2024-05-04 16:08:04.039][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:08:04.041][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.042][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2024-05-04 16:08:04.043][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:08:04.044][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2024-05-04 16:08:04.044][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2024-05-04 16:08:04.045][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:04.047][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:04.048][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 16:08:04.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:04.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:04.051][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:08:04.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:04.053][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:04.055][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:08:04.056][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2024-05-04 16:08:04.056][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2024-05-04 16:08:04.057][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:08:04.058][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:08:04.059][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.060][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:04.062][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2024-05-04 16:08:04.064][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.065][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2024-05-04 16:08:04.066][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.067][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:08:04.069][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.070][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:08:04.071][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.072][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:08:04.074][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 16:08:04.075][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:08:04.076][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.077][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2024-05-04 16:08:04.079][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:08:04.080][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2024-05-04 16:08:04.080][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2024-05-04 16:08:04.080][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2024-05-04 16:08:04.080][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2024-05-04 16:08:04.080][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2024-05-04 16:08:04.080][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2024-05-04 16:08:04.081][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:04.082][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:08:04.089][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 16:08:04.091][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:04.092][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:04.093][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:08:04.094][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:04.095][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:04.096][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:08:04.098][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2024-05-04 16:08:04.098][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2024-05-04 16:08:04.099][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:08:04.100][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:08:04.101][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.102][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:04.104][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2024-05-04 16:08:04.106][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:04.107][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2024-05-04 16:08:04.108][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.109][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:08:04.110][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.111][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:08:04.113][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.114][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:08:04.115][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 16:08:04.116][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:08:04.117][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.119][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2024-05-04 16:08:04.120][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:08:04.121][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2024-05-04 16:08:04.121][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:08:04.121][self$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[2024-05-04 16:08:04.121][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:08:04.121][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:08:04.121][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:08:04.121][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:08:04.121][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:08:04.121][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:08:04.121][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:08:04.121][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2024-05-04 16:08:04.121][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:08:04.121][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:08:04.121][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2024-05-04 16:08:04.122][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:04.124][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:08:04.124][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:08:04.124][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:08:04.125][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2024-05-04 16:08:04.126][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:04.127][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:04.128][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:08:04.129][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:04.130][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:04.132][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:08:04.133][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2024-05-04 16:08:04.133][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2024-05-04 16:08:04.133][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2024-05-04 16:08:04.134][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:08:04.135][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:08:04.136][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.137][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2024-05-04 16:08:04.139][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2024-05-04 16:08:04.141][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.142][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2024-05-04 16:08:04.143][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.144][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:08:04.146][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.147][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:08:04.148][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.149][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:08:04.150][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 16:08:04.151][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:08:04.153][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.154][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2024-05-04 16:08:04.155][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:08:04.156][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2024-05-04 16:08:04.156][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2024-05-04 16:08:04.157][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:08:04.159][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:08:04.160][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2024-05-04 16:08:04.161][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:04.162][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:04.163][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:08:04.164][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:08:04.165][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:08:04.166][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:08:04.168][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2024-05-04 16:08:04.168][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2024-05-04 16:08:04.168][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2024-05-04 16:08:04.169][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:08:04.170][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:08:04.171][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:08:04.172][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2024-05-04 16:08:04.174][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2024-05-04 16:08:04.175][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 16:08:04.177][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 16:08:04.179][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2024-05-04 16:08:04.181][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 16:08:04.182][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2024-05-04 16:08:04.188][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2024-05-04 16:08:04.189][super$initialize] Register connector ncbi.pubchem.subst with the request scheduler
biodb.DEBUG[2024-05-04 16:08:04.190][private$bdb$getRequestScheduler()$re ...] Register connector ncbi.pubchem.subst.
biodb.DEBUG[2024-05-04 16:08:04.192][private$addConnectorRules] Create new rule for URL "pubchem.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.subst".
biodb.DEBUG[2024-05-04 16:08:04.193][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2024-05-04 16:08:04.195][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2024-05-04 16:08:04.196][private$addConnectorRules] Create new rule for URL "eutils.ncbi.nlm.nih.gov" of connector "ncbi.pubchem.subst".
biodb.DEBUG[2024-05-04 16:08:04.198][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2024-05-04 16:08:04.199][self$setFrequency] t=1.000000, n=5.000000
biodb.DEBUG[2024-05-04 16:08:04.201][rule$addConnector] Connector "ncbi.pubchem.subst" is already listed in rule "pubchem.ncbi.nlm.nih.gov".
biodb.DEBUG[2024-05-04 16:08:04.206][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2024-05-04 16:08:04.212][biodb::testThat]
biodb.INFO [2024-05-04 16:08:04.213][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-04 16:08:04.214][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:08:04.215][biodb::testThat]
biodb.TRACE[2024-05-04 16:08:04.219][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2024-05-04 16:08:04.220][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2024-05-04 16:08:04.224][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2024-05-04 16:08:04.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:04.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:04.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:04.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:04.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:04.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:04.238][FUN] Functions in observer BiodbConfig: [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[2024-05-04 16:08:04.241][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.242][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.244][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.251][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.252][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.254][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.256][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.261][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.266][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.275][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:08:04.309][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2024-05-04 16:08:04.311][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:08:04.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:08:04.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.316][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:08:04.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:08:04.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.321][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:08:04.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:08:04.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.326][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:08:04.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:08:04.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.331][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:08:04.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:08:04.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.335][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 16:08:04.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 16:08:04.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.340][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 16:08:04.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 16:08:04.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.359][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.401][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.406][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.411][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.440][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.441][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.444][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.466][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.471][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.476][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.480][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.482][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.484][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.485][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.500][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.501][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.503][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.510][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.512][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.514][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 16:08:04.527][biodb::testThat]
biodb.INFO [2024-05-04 16:08:04.528][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-04 16:08:04.529][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:08:04.531][biodb::testThat]
biodb.DEBUG[2024-05-04 16:08:04.533][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2024-05-04 16:08:04.535][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 16:08:04.541][cch$loadFileContent] Trying to load 1 files from cache: [1]: "3".
biodb.TRACE[2024-05-04 16:08:04.543][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 16:08:04.554][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75/3.xml".
biodb.DEBUG[2024-05-04 16:08:04.556][conn$getEntryContent] 1 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 16:08:04.557][self$createEntryFromContent] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2024-05-04 16:08:04.559][self$createEntryFromContent] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2024-05-04 16:08:04.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:08:04.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:04.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:04.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:04.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:04.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:04.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:08:04.576][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.577][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.579][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.586][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.587][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.590][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.591][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-04 16:08:04.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.596][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.601][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.611][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2024-05-04 16:08:04.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:08:04.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:08:04.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:08:04.646][self$createEntryFromContent] Accession numbers: 3.
biodb.TRACE[2024-05-04 16:08:04.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-04 16:08:04.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-04 16:08:04.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-04 16:08:04.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-04 16:08:04.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-04 16:08:04.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-04 16:08:04.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 16:08:04.675][biodb::testThat]
biodb.INFO [2024-05-04 16:08:04.677][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-04 16:08:04.678][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:08:04.679][biodb::testThat]
biodb.INFO [2024-05-04 16:08:04.688][biodb::testThat]
biodb.INFO [2024-05-04 16:08:04.689][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-04 16:08:04.690][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:08:04.691][biodb::testThat]
biodb.WARN [2024-05-04 16:08:04.695][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-05-04 16:08:04.699][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-05-04 16:08:04.711][biodb::testThat]
biodb.INFO [2024-05-04 16:08:04.713][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-04 16:08:04.714][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:08:04.715][biodb::testThat]
biodb.TRACE[2024-05-04 16:08:04.728][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:08:04.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:08:04.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.733][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:08:04.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:08:04.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.738][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:08:04.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:08:04.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.743][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:08:04.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:08:04.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.748][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:08:04.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:08:04.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.752][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 16:08:04.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 16:08:04.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.757][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 16:08:04.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 16:08:04.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.763][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:08:04.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:08:04.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.768][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2024-05-04 16:08:04.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2024-05-04 16:08:04.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.773][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:08:04.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2024-05-04 16:08:04.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.778][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:08:04.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:08:04.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.783][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:08:04.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:08:04.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.788][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 16:08:04.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 16:08:04.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:08:04.792][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 16:08:04.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 16:08:04.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:08:04.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 16:08:04.805][biodb::testThat]
biodb.INFO [2024-05-04 16:08:04.806][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-04 16:08:04.807][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:08:04.809][biodb::testThat]
biodb.INFO [2024-05-04 16:08:04.819][biodb::testThat]
biodb.INFO [2024-05-04 16:08:04.821][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-04 16:08:04.822][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:08:04.823][biodb::testThat]
biodb.INFO [2024-05-04 16:08:04.834][biodb::testThat]
biodb.INFO [2024-05-04 16:08:04.835][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-04 16:08:04.837][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:08:04.838][biodb::testThat]
biodb.DEBUG[2024-05-04 16:08:04.842][function(conn, opt)] Trying to download "https://pubchem.ncbi.nlm.nih.gov/substance/3".
biodb.DEBUG[2024-05-04 16:08:04.920][getUrlContent] Use RCurl for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/substance/3.
biodb.INFO [2024-05-04 16:08:05.056][biodb::testThat]
biodb.INFO [2024-05-04 16:08:05.057][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-04 16:08:05.058][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:08:05.060][biodb::testThat]
biodb.DEBUG[2024-05-04 16:08:05.150][getUrlContent] Use RCurl for downloading content of URL https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?sid=3&t=l.
biodb.INFO [2024-05-04 16:08:05.219][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-04 16:08:05.221][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector ncbi.pubchem.subst from the request scheduler
biodb.INFO [2024-05-04 16:08:05.223][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2024-05-04 16:08:05.224][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-04 16:08:05.225][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:08:05.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:08:05.227][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:08:05.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:08:05.229][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:08:05.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 17 | WARN 8 | SKIP 0 | PASS 353 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_ccds.R:37:1'): RT unit is defined when there is an RT value. ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$doGetEntryContentOneByOne(id)
  9.               └─scheduler$sendRequest(requests[[i]])
 10.                 └─cch$saveContentToFile(...)
 11.                   └─private$doSaveContentToFile(...)
 12.                     └─biodb:::saveContentsToFiles(file.paths, content)
 13.                       └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 14.                         └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 15.                           └─base::cat(cnt, file = f)
 16.                             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_100_ccds.R:37:1'): We can load an entry from the database. ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─cch$saveContentToFile(...)
  9.               └─private$doSaveContentToFile(...)
 10.                 └─biodb:::saveContentsToFiles(file.paths, content)
 11.                   └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 12.                     └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 13.                       └─base::cat(cnt, file = f)
 14.                         └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_200_gene.R:37:1'): Entry fields have a correct value ──────
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$saveEntriesAsJson(id, list(e))
  4.     └─private$bdb$saveEntriesAsJson(entries, json.files)
  5.       └─entries[[i]]$getFieldsAsJson(compute = compute)
  6.         └─self$computeFields()
  7.           └─private$computeField(f)
  8.             └─self$getBiodb()$getFactory()$getEntry(db, id = db.id)
  9.               └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 10.                 └─conn$getEntryContent(ids)
 11.                   └─self$getEntryContentFromDb(ch.missing.ids)
 12.                     └─private$doGetEntryContentFromDb(entry.id)
 13.                       └─private$doGetEntryContentOneByOne(id)
 14.                         └─scheduler$sendRequest(requests[[i]])
 15.                           └─cch$saveContentToFile(...)
 16.                             └─private$doSaveContentToFile(...)
 17.                               └─biodb:::saveContentsToFiles(file.paths, content)
 18.                                 └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 19.                                   └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 20.                                     └─base::cat(cnt, file = f)
 21.                                       └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_200_gene.R:37:1'): RT unit is defined when there is an RT value. ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─cch$saveContentToFile(...)
  7.           └─private$doSaveContentToFile(...)
  8.             └─biodb:::saveContentsToFiles(file.paths, content)
  9.               └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 10.                 └─biodb (local) `<fn>`(dots[[1L]][[5L]], dots[[2L]][[5L]])
 11.                   └─base::cat(cnt, file = f)
 12.                     └─base::file(file, ifelse(append, "a", "w"))
── Failure ('test_long_200_gene.R:37:1'): We can search for an entry by searchable field ──
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by searchable field ──
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
── Failure ('test_long_200_gene.R:37:1'): We can search for an entry by name. ──
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by name. ────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
── Failure ('test_long_200_gene.R:37:1'): We can load an entry from the database. ──
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure ('test_long_200_gene.R:37:1'): We can load an entry from the database. ──
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by name. ──
Error in `XML::xmlInternalTreeParse(results, asText = TRUE)`: empty or no content specified
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$searchByName(name = name, max.results = max.results)
 4.     └─self$searchForEntries(list(name = name), max.results = max.results)
 5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
 6.         └─self$wsEsearch(term = term, retmax = retmax, retfmt = "ids")
 7.           └─XML::xmlInternalTreeParse(results, asText = TRUE)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for a compound ───
Error in `XML::xmlInternalTreeParse(results, asText = TRUE)`: empty or no content specified
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(db = `<NcbPbcCC>`, opt = `<named list>`)
  3.   ├─lifecycle::expect_deprecated(db$searchCompound(name = name, max.results = max.results))
  4.   │ └─testthat::expect_warning(...)
  5.   │   └─testthat:::quasi_capture(...)
  6.   │     ├─testthat (local) .capture(...)
  7.   │     │ └─base::withCallingHandlers(...)
  8.   │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  9.   └─db$searchCompound(name = name, max.results = max.results)
 10.     └─self$searchForEntries(list(name = name), max.results = max.results)
 11.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
 12.         └─self$wsEsearch(term = term, retmax = retmax, retfmt = "ids")
 13.           └─XML::xmlInternalTreeParse(results, asText = TRUE)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() accepts a single vector. ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
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.           └─self$getBiodb()$getRequestScheduler()$sendRequest(request)
  8.             └─cch$saveContentToFile(...)
  9.               └─private$doSaveContentToFile(...)
 10.                 └─biodb:::saveContentsToFiles(file.paths, content)
 11.                   └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 12.                     └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 13.                       └─base::cat(cnt, file = f)
 14.                         └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_300_pubchem.comp.R:37:1'): ppm tolerance works in annotateMzValues() ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$annotateMzValues(...)
  4.     └─self$searchForEntries(fieldsFilter, max.results = max.results)
  5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
  6.         └─self$wsEsearch(term = term, retmax = retmax, retfmt = "ids")
  7.           └─self$getBiodb()$getRequestScheduler()$sendRequest(request)
  8.             └─cch$saveContentToFile(...)
  9.               └─private$doSaveContentToFile(...)
 10.                 └─biodb:::saveContentsToFiles(file.paths, content)
 11.                   └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 12.                     └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 13.                       └─base::cat(cnt, file = f)
 14.                         └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_300_pubchem.comp.R:37:1'): Input data frame is not modified by annotateMzValues() ──
Error in `XML::xmlInternalTreeParse(results, asText = TRUE)`: empty or no content specified
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 `file(file, ifelse(append, "a", "w"))`: cannot open the connection
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.           └─self$getBiodb()$getRequestScheduler()$sendRequest(request)
  8.             └─cch$saveContentToFile(...)
  9.               └─private$doSaveContentToFile(...)
 10.                 └─biodb:::saveContentsToFiles(file.paths, content)
 11.                   └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 12.                     └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 13.                       └─base::cat(cnt, file = f)
 14.                         └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_300_pubchem.comp.R:37:1'): Additional fields are accepted in annotateMzValues() ──
Error in `XML::xmlInternalTreeParse(results, asText = TRUE)`: empty or no content specified
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$annotateMzValues(...)
 4.     └─self$searchForEntries(fieldsFilter, max.results = max.results)
 5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
 6.         └─self$wsEsearch(term = term, retmax = retmax, retfmt = "ids")
 7.           └─XML::xmlInternalTreeParse(results, asText = TRUE)

[ FAIL 17 | WARN 8 | SKIP 0 | PASS 353 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNcbi.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'biodbNcbi/DESCRIPTION' ... OK
* this is package 'biodbNcbi' version '1.8.0'
* 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:
  ── Error ('test_long_300_pubchem.comp.R:37:1'): Additional fields are accepted in annotateMzValues() ──
  Error in `XML::xmlInternalTreeParse(results, asText = TRUE)`: empty or no content specified
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
   3.   └─conn$annotateMzValues(...)
   4.     └─self$searchForEntries(fieldsFilter, max.results = max.results)
   5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
   6.         └─self$wsEsearch(term = term, retmax = retmax, retfmt = "ids")
   7.           └─XML::xmlInternalTreeParse(results, asText = TRUE)
  
  [ FAIL 17 | WARN 8 | SKIP 0 | PASS 353 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.19-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)