Back to Long Tests report for BioC 3.19

This page was generated on 2024-06-22 23:55 -0400 (Sat, 22 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
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 12/33HostnameOS / ArchCHECK
biodbNci 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-22 09:55 -0400 (Sat, 22 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_19
git_last_commit: 0db4525
git_last_commit_date: 2024-04-30 11:41:04 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.7.4 Monterey / x86_64  OK  

CHECK results for biodbNci on merida1

To the developers/maintainers of the biodbNci 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: biodbNci
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz
StartedAt: 2024-06-22 16:02:25 -0400 (Sat, 22 Jun 2024)
EndedAt: 2024-06-22 16:03:52 -0400 (Sat, 22 Jun 2024)
EllapsedTime: 86.6 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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Type 'contributors()' for more information and
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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("biodbNci")
biodb.INFO [2024-06-22 16:03:48.184][biodb::testContext]
biodb.INFO [2024-06-22 16:03:48.188][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:03:48.189][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-22 16:03:48.191][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:03:48.192][biodb::testContext]
biodb.INFO [2024-06-22 16:03:48.200][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:03:48.202][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-22 16:03:48.210][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:03:48.212][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-22 16:03:48.213][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-22 16:03:48.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.218][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-22 16:03:48.246][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-22 16:03:48.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.250][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-22 16:03:48.252][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-22 16:03:48.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.257][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-22 16:03:48.258][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-22 16:03:48.259][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-22 16:03:48.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.264][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-22 16:03:48.265][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-22 16:03:48.267][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-22 16:03:48.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.272][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-22 16:03:48.273][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-22 16:03:48.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.276][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[2024-06-22 16:03:48.278][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-22 16:03:48.279][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-22 16:03:48.280][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-22 16:03:48.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.285][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-22 16:03:48.286][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-22 16:03:48.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.291][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-22 16:03:48.292][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-22 16:03:48.293][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-22 16:03:48.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.298][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:03:48.299][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-22 16:03:48.300][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-22 16:03:48.302][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-22 16:03:48.303][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-22 16:03:48.304][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-22 16:03:48.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.308][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[2024-06-22 16:03:48.309][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-22 16:03:48.310][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-22 16:03:48.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.315][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-22 16:03:48.316][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-22 16:03:48.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.321][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-22 16:03:48.322][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-22 16:03:48.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.327][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-22 16:03:48.328][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-22 16:03:48.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.333][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-22 16:03:48.334][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-22 16:03:48.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.339][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:03:48.340][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-22 16:03:48.350][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-22 16:03:48.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.355][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-22 16:03:48.356][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-22 16:03:48.358][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-22 16:03:48.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.365][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-22 16:03:48.410][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.438][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-22 16:03:48.439][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.440][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:03:48.442][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.443][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.444][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.445][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.446][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:03:48.448][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:03:48.449][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.450][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-22 16:03:48.451][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:03:48.453][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.454][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.455][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:03:48.455][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:03:48.455][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:03:48.455][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:03:48.455][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:03:48.457][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:03:48.458][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.460][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:03:48.461][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.462][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.463][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.465][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.466][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:03:48.467][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:03:48.468][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.469][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.471][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-22 16:03:48.473][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.474][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:03:48.476][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.477][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:03:48.478][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.479][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.481][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.483][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.484][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:03:48.485][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:03:48.487][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.488][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-22 16:03:48.490][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:03:48.491][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.492][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.494][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:03:48.494][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:03:48.494][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:03:48.494][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:03:48.494][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:03:48.495][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:03:48.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.500][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:03:48.503][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.504][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.505][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.506][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.507][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:03:48.508][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:03:48.511][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.512][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.514][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-22 16:03:48.516][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.517][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-22 16:03:48.519][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.520][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:03:48.521][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.522][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.523][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.525][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.526][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:03:48.532][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:03:48.533][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.534][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-22 16:03:48.536][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:03:48.537][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.538][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.539][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.541][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:03:48.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.544][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:03:48.545][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.547][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.548][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.549][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.550][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:03:48.552][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:03:48.553][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.555][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.556][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-22 16:03:48.558][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.559][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:03:48.561][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.562][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:03:48.563][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.564][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.565][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.567][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.568][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:03:48.569][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:03:48.570][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.572][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-22 16:03:48.573][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:03:48.574][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.575][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.577][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.578][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:03:48.579][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.580][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.581][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:03:48.583][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.584][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.585][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.586][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.588][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:03:48.589][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:03:48.590][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.591][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.595][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:03:48.597][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.598][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[2024-06-22 16:03:48.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.604][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[2024-06-22 16:03:48.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.644][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[2024-06-22 16:03:48.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.666][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[2024-06-22 16:03:48.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.677][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[2024-06-22 16:03:48.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.684][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[2024-06-22 16:03:48.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.690][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[2024-06-22 16:03:48.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.695][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.DEBUG[2024-06-22 16:03:48.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.702][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-22 16:03:48.707][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-22 16:03:48.709][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-22 16:03:48.711][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-22 16:03:48.713][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-22 16:03:48.714][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-22 16:03:48.716][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-22 16:03:48.718][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-22 16:03:48.719][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-22 16:03:48.721][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-22 16:03:48.723][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-22 16:03:48.724][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-22 16:03:48.726][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-22 16:03:48.728][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-22 16:03:48.729][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-22 16:03:48.731][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-22 16:03:48.733][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-22 16:03:48.735][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-22 16:03:48.736][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-22 16:03:48.738][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-22 16:03:48.740][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-22 16:03:48.742][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-22 16:03:48.744][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-22 16:03:48.745][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-22 16:03:48.747][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-22 16:03:48.749][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-22 16:03:48.751][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-22 16:03:48.752][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-22 16:03:48.754][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-22 16:03:48.756][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-22 16:03:48.758][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-22 16:03:48.759][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-22 16:03:48.761][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-22 16:03:48.763][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-22 16:03:48.764][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-22 16:03:48.766][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-22 16:03:48.768][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-22 16:03:48.770][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-22 16:03:48.771][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-22 16:03:48.773][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-22 16:03:48.775][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-22 16:03:48.776][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-22 16:03:48.778][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-22 16:03:48.780][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-22 16:03:48.782][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-22 16:03:48.783][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-22 16:03:48.785][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-22 16:03:48.787][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-22 16:03:48.789][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-22 16:03:48.791][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-22 16:03:48.792][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-22 16:03:48.794][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-22 16:03:48.796][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-22 16:03:48.797][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-22 16:03:48.799][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-22 16:03:48.801][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-22 16:03:48.803][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-22 16:03:48.804][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-22 16:03:48.806][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-22 16:03:48.808][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-22 16:03:48.810][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-22 16:03:48.812][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-22 16:03:48.813][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-22 16:03:48.815][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-22 16:03:48.817][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-22 16:03:48.819][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-22 16:03:48.821][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-22 16:03:48.823][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-22 16:03:48.824][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-22 16:03:48.826][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-22 16:03:48.828][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-22 16:03:48.829][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-22 16:03:48.831][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-22 16:03:48.833][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-22 16:03:48.835][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-22 16:03:48.836][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-22 16:03:48.838][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-22 16:03:48.840][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-22 16:03:48.841][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-22 16:03:48.843][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-22 16:03:48.845][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-22 16:03:48.847][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-22 16:03:48.848][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-22 16:03:48.857][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-22 16:03:48.859][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:03:48.862][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:03:48.863][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.865][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.907][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[2024-06-22 16:03:48.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.914][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[2024-06-22 16:03:48.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.922][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[2024-06-22 16:03:48.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.929][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[2024-06-22 16:03:48.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.937][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[2024-06-22 16:03:48.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.944][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[2024-06-22 16:03:48.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.952][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[2024-06-22 16:03:48.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.959][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[2024-06-22 16:03:48.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.967][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[2024-06-22 16:03:48.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.975][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[2024-06-22 16:03:48.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.990][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[2024-06-22 16:03:48.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:49.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:49.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:49.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:49.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:49.005][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[2024-06-22 16:03:49.007][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-06-22 16:03:49.020][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-06-22 16:03:49.023][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-06-22 16:03:49.025][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:49.026][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:03:49.027][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:49.029][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-06-22 16:03:49.030][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:49.031][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:03:49.032][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-06-22 16:03:49.033][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:03:49.035][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:49.036][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-06-22 16:03:49.037][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:03:49.038][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-06-22 16:03:49.038][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-06-22 16:03:49.038][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-06-22 16:03:49.038][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-06-22 16:03:49.038][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-06-22 16:03:49.038][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-06-22 16:03:49.038][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-06-22 16:03:49.040][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:49.041][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:49.042][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-22 16:03:49.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:49.045][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:49.046][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:03:49.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:49.048][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:49.050][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:03:49.051][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-22 16:03:49.051][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-22 16:03:49.051][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-06-22 16:03:49.051][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-06-22 16:03:49.052][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:03:49.053][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:03:49.054][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:49.056][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:49.064][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-06-22 16:03:49.087][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-06-22 16:03:49.089][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-06-22 16:03:49.093][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-06-22 16:03:49.098][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-06-22 16:03:49.103][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:03:49.104][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:03:49.106][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-22 16:03:49.107][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-22 16:03:49.109][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-22 16:03:49.110][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-06-22 16:03:49.150][biodb::testThat]
biodb.INFO [2024-06-22 16:03:49.151][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-22 16:03:49.152][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:49.154][biodb::testThat]
biodb.TRACE[2024-06-22 16:03:49.157][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-06-22 16:03:49.160][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-06-22 16:03:49.163][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-06-22 16:03:49.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:03:49.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:49.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:49.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:49.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:49.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:49.192][FUN] Functions in observer BiodbConfig: [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[2024-06-22 16:03:49.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.241][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.281][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:49.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:49.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:49.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:49.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.308][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.313][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.319][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:49.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:49.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.324][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:49.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:49.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.334][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:49.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:49.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:49.421][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-06-22 16:03:49.424][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:03:49.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:03:49.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.429][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:03:49.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:03:49.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.433][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:03:49.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:03:49.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.438][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:03:49.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:03:49.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.481][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:49.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:49.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.523][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:49.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:49.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.528][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:49.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:49.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.533][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:49.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:49.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.566][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.568][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.570][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.587][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.592][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.597][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.602][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.603][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.606][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.607][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.627][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.637][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.639][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.641][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:49.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:49.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:49.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:49.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.668][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:49.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:49.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.673][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:49.675][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:49.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.677][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:49.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:49.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.695][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.701][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.706][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.711][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.712][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.714][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.715][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.730][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.731][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.734][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.744][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.746][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.748][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.754][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:49.756][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:49.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.758][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.764][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.765][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.768][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.774][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.775][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.778][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.801][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-06-22 16:03:49.849][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-06-22 16:03:49.851][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-06-22 16:03:49.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:03:49.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:49.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:49.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:49.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:49.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:49.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-22 16:03:49.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.914][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:49.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:49.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.923][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:49.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:49.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.929][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.933][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:49.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.949][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.963][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.973][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.978][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.984][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:49.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:49.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:49.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:49.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.001][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.007][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.012][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.022][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:50.057][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-06-22 16:03:50.085][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:03:50.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:03:50.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.090][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:03:50.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:03:50.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.095][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:03:50.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:03:50.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.100][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:03:50.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:03:50.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.119][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.163][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.168][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.173][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.216][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.217][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.219][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.236][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.241][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.246][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.251][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.252][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.254][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.256][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.276][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.281][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.286][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.287][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.289][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.291][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.310][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.315][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.320][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.325][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.326][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.329][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.330][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.361][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.362][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.365][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.386][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.391][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.396][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.398][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.400][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.422][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.427][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.432][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.433][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.436][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.437][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.451][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.453][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.455][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.461][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.463][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.465][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.471][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.473][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.475][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.481][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.483][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.484][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.485][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.496][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.497][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.499][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.506][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.507][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.509][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.515][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.517][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.519][ef$get] fields variable is a list.
biodb.INFO [2024-06-22 16:03:50.529][biodb::testThat]
biodb.INFO [2024-06-22 16:03:50.530][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-22 16:03:50.532][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:50.533][biodb::testThat]
biodb.DEBUG[2024-06-22 16:03:50.535][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-06-22 16:03:50.543][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-06-22 16:03:50.548][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2024-06-22 16:03:50.550][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2024-06-22 16:03:50.553][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-06-22 16:03:50.554][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-06-22 16:03:50.557][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2024-06-22 16:03:50.558][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-06-22 16:03:50.559][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-06-22 16:03:50.561][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-06-22 16:03:50.563][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:03:50.564][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:50.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:50.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:50.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:50.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:50.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-22 16:03:50.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.599][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.605][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.627][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.638][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.644][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.649][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.659][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:50.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:03:50.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:50.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:50.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:50.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:50.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:50.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-22 16:03:50.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.723][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.728][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.734][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.740][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-22 16:03:50.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.772][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.777][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.794][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.799][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.805][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.816][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.821][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.832][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-22 16:03:50.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:50.883][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-06-22 16:03:50.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-22 16:03:50.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-22 16:03:50.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:03:50.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:03:50.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:03:50.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:03:50.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-22 16:03:50.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-22 16:03:50.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:03:50.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:03:50.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:03:50.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:03:50.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-22 16:03:50.932][biodb::testThat]
biodb.INFO [2024-06-22 16:03:50.934][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-22 16:03:50.935][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:50.936][biodb::testThat]
biodb.INFO [2024-06-22 16:03:50.944][biodb::testThat]
biodb.INFO [2024-06-22 16:03:50.945][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-22 16:03:50.947][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:50.948][biodb::testThat]
biodb.WARN [2024-06-22 16:03:50.975][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-06-22 16:03:51.001][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-06-22 16:03:51.013][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.015][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-22 16:03:51.016][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:51.017][biodb::testThat]
biodb.TRACE[2024-06-22 16:03:51.049][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.054][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.059][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:03:51.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:03:51.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.064][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:03:51.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:03:51.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.120][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.125][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.130][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:03:51.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:03:51.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.135][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:03:51.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:03:51.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-22 16:03:51.147][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.148][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-22 16:03:51.149][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:51.150][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.160][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.161][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-22 16:03:51.162][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:51.164][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.173][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.174][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-22 16:03:51.175][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:51.177][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.184][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.186][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-22 16:03:51.187][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:51.188][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.196][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-22 16:03:51.197][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-06-22 16:03:51.198][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-06-22 16:03:51.199][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-22 16:03:51.200][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.203][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.205][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.207][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.INFO [2024-06-22 16:03:51.219][biodb::testContext]
biodb.INFO [2024-06-22 16:03:51.221][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:03:51.222][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-22 16:03:51.223][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:03:51.224][biodb::testContext]
biodb.INFO [2024-06-22 16:03:51.227][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:03:51.228][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-22 16:03:51.233][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:03:51.234][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-22 16:03:51.235][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-22 16:03:51.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.241][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-22 16:03:51.242][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-22 16:03:51.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.251][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-22 16:03:51.252][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-22 16:03:51.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.257][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-22 16:03:51.258][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-22 16:03:51.259][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-22 16:03:51.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.264][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-22 16:03:51.265][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-22 16:03:51.267][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-22 16:03:51.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.271][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-22 16:03:51.272][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-22 16:03:51.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.276][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[2024-06-22 16:03:51.277][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-22 16:03:51.278][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-22 16:03:51.279][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-22 16:03:51.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.284][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-22 16:03:51.285][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-22 16:03:51.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.289][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-22 16:03:51.291][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-22 16:03:51.292][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-22 16:03:51.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.296][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:03:51.298][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-22 16:03:51.299][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-22 16:03:51.300][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-22 16:03:51.301][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-22 16:03:51.303][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-22 16:03:51.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.307][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-22 16:03:51.308][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-22 16:03:51.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.313][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-22 16:03:51.314][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-22 16:03:51.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.319][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-22 16:03:51.320][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-22 16:03:51.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.325][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-22 16:03:51.326][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-22 16:03:51.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.331][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-22 16:03:51.332][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-22 16:03:51.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.336][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:03:51.338][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-22 16:03:51.348][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-22 16:03:51.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.352][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[2024-06-22 16:03:51.353][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-22 16:03:51.355][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-22 16:03:51.356][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-22 16:03:51.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.361][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-22 16:03:51.363][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:51.365][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-22 16:03:51.366][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.367][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:03:51.369][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.370][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:03:51.371][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:51.372][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:03:51.374][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:03:51.375][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:03:51.376][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.377][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-22 16:03:51.379][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:03:51.380][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.381][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.382][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:03:51.382][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:03:51.382][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:03:51.382][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:03:51.382][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:03:51.384][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:03:51.385][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:51.386][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:51.387][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:03:51.388][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:51.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:51.391][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:03:51.392][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.393][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:03:51.394][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:03:51.396][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:51.397][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.398][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-22 16:03:51.401][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:51.402][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:03:51.403][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.404][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:03:51.405][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.407][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:03:51.408][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:51.409][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:03:51.410][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:03:51.412][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:03:51.413][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.414][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-22 16:03:51.415][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:03:51.417][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.418][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.419][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:03:51.419][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:03:51.419][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:03:51.419][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:03:51.419][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:03:51.420][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:03:51.422][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:51.423][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:51.424][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:03:51.425][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:51.426][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:51.427][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:03:51.429][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.434][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:03:51.435][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:03:51.436][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:51.437][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.439][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-22 16:03:51.441][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.442][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-22 16:03:51.443][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.445][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:03:51.446][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.447][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:03:51.448][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:51.450][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:03:51.451][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:03:51.452][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:03:51.453][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:51.454][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-22 16:03:51.456][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:03:51.457][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.458][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.459][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.460][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:03:51.462][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:51.463][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:51.464][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:03:51.465][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:51.466][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:51.467][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:03:51.469][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.470][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:03:51.471][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:03:51.472][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:51.474][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.475][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-22 16:03:51.477][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.479][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:03:51.480][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.481][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:03:51.483][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.484][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:03:51.485][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:51.486][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:03:51.488][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:03:51.489][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:03:51.490][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:51.491][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-22 16:03:51.493][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:03:51.494][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.495][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.496][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.498][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:03:51.499][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:51.500][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:51.501][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:03:51.502][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:51.503][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:51.505][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:03:51.506][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.507][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:03:51.508][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:03:51.509][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:51.511][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.512][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:03:51.513][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.543][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.DEBUG[2024-06-22 16:03:51.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.616][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[2024-06-22 16:03:51.617][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-22 16:03:51.619][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-22 16:03:51.620][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-22 16:03:51.622][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-22 16:03:51.624][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-22 16:03:51.625][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-22 16:03:51.627][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-22 16:03:51.629][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-22 16:03:51.631][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-22 16:03:51.632][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-22 16:03:51.634][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-22 16:03:51.636][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-22 16:03:51.638][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-22 16:03:51.639][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-22 16:03:51.641][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-22 16:03:51.643][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-22 16:03:51.644][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-22 16:03:51.646][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-22 16:03:51.648][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-22 16:03:51.650][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-22 16:03:51.651][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-22 16:03:51.653][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-22 16:03:51.655][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-22 16:03:51.657][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-22 16:03:51.658][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-22 16:03:51.660][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-22 16:03:51.662][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-22 16:03:51.663][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-22 16:03:51.665][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-22 16:03:51.667][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-22 16:03:51.669][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-22 16:03:51.671][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-22 16:03:51.673][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-22 16:03:51.674][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-22 16:03:51.676][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-22 16:03:51.678][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-22 16:03:51.679][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-22 16:03:51.681][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-22 16:03:51.683][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-22 16:03:51.685][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-22 16:03:51.686][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-22 16:03:51.688][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-22 16:03:51.690][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-22 16:03:51.692][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-22 16:03:51.693][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-22 16:03:51.695][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-22 16:03:51.697][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-22 16:03:51.699][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-22 16:03:51.701][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-22 16:03:51.703][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-22 16:03:51.705][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-22 16:03:51.707][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-22 16:03:51.709][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-22 16:03:51.710][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-22 16:03:51.712][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-22 16:03:51.714][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-22 16:03:51.716][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-22 16:03:51.718][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-22 16:03:51.720][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-22 16:03:51.722][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-22 16:03:51.723][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-22 16:03:51.725][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-22 16:03:51.727][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-22 16:03:51.729][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-22 16:03:51.730][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-22 16:03:51.732][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-22 16:03:51.734][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-22 16:03:51.736][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-22 16:03:51.737][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-22 16:03:51.739][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-22 16:03:51.741][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-22 16:03:51.742][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-22 16:03:51.744][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-22 16:03:51.746][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-22 16:03:51.748][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-22 16:03:51.749][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-22 16:03:51.751][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-22 16:03:51.753][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-22 16:03:51.754][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-22 16:03:51.756][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-22 16:03:51.758][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-22 16:03:51.760][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-22 16:03:51.761][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-22 16:03:51.763][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-22 16:03:51.765][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:03:51.766][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:03:51.767][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.770][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.863][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[2024-06-22 16:03:51.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.885][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[2024-06-22 16:03:51.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:51.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:51.911][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-06-22 16:03:51.912][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-06-22 16:03:51.915][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:51.916][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-06-22 16:03:51.917][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.918][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:03:51.919][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:51.921][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-06-22 16:03:51.922][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.923][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:03:51.924][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-06-22 16:03:51.926][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:03:51.927][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.928][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-06-22 16:03:51.930][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:03:51.931][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-06-22 16:03:51.931][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-06-22 16:03:51.931][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-06-22 16:03:51.931][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-06-22 16:03:51.931][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-06-22 16:03:51.931][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-06-22 16:03:51.931][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-06-22 16:03:51.932][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:51.934][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.935][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-22 16:03:51.936][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:51.937][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:51.938][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:03:51.939][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:51.940][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:51.942][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:03:51.943][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-22 16:03:51.943][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-22 16:03:51.943][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-06-22 16:03:51.943][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-06-22 16:03:51.948][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:03:51.949][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:03:51.950][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:51.951][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:51.953][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-06-22 16:03:51.957][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-06-22 16:03:51.958][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-06-22 16:03:51.959][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-06-22 16:03:51.961][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-06-22 16:03:51.962][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:03:51.964][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:03:51.965][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-22 16:03:51.967][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-22 16:03:51.968][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-22 16:03:51.969][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-06-22 16:03:51.971][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-22 16:03:51.972][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-06-22 16:03:51.973][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-06-22 16:03:51.974][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-22 16:03:51.975][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:51.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:51.977][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:51.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:51.980][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:51.981][FUN] Functions in observer 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 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  5.816   0.330   6.144

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: OK

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractEntries.cpp -o extractEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-example.cpp -o test-100-example.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)