Back to Long Tests report for BioC 3.20

This page was generated on 2024-07-06 23:55 -0400 (Sat, 06 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4643
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4414
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4442
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 11/32HostnameOS / ArchCHECK
biodbNci 1.9.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-07-06 09:55 -0400 (Sat, 06 Jul 2024)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 12acfea
git_last_commit_date: 2024-04-30 11:41:04 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino6Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  


CHECK results for biodbNci on nebbiolo2

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: 1.9.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.9.0.tar.gz
StartedAt: 2024-07-06 16:04:30 -0400 (Sat, 06 Jul 2024)
EndedAt: 2024-07-06 16:05:36 -0400 (Sat, 06 Jul 2024)
EllapsedTime: 66.1 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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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 [2024-07-06 16:05:32.935][biodb::testContext]
biodb.INFO [2024-07-06 16:05:32.937][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:05:32.938][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-07-06 16:05:32.938][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:05:32.939][biodb::testContext]
biodb.INFO [2024-07-06 16:05:32.945][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:05:32.947][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-06 16:05:32.954][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:05:32.955][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-06 16:05:32.956][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-06 16:05:32.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:32.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:32.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:32.959][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-06 16:05:32.976][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-06 16:05:32.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:32.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:32.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:32.979][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-06 16:05:32.980][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-06 16:05:32.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:32.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:32.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:32.984][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-06 16:05:32.984][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-06 16:05:32.985][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-06 16:05:32.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:32.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:32.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:32.989][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-06 16:05:32.989][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-06 16:05:32.990][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-06 16:05:32.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:32.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:32.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:32.994][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-06 16:05:32.994][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-06 16:05:32.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:32.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:32.997][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[2024-07-06 16:05:32.998][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-06 16:05:32.999][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-06 16:05:32.999][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-06 16:05:33.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.003][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-06 16:05:33.004][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-06 16:05:33.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.007][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-06 16:05:33.008][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-06 16:05:33.009][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-06 16:05:33.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.012][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:05:33.013][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-06 16:05:33.014][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-06 16:05:33.015][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-06 16:05:33.015][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-06 16:05:33.016][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-06 16:05:33.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.020][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-06 16:05:33.021][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-06 16:05:33.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.024][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-06 16:05:33.025][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-06 16:05:33.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.028][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-06 16:05:33.029][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-06 16:05:33.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.032][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-06 16:05:33.033][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-06 16:05:33.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.036][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-06 16:05:33.037][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-06 16:05:33.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.040][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:05:33.041][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-06 16:05:33.044][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-06 16:05:33.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.048][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-06 16:05:33.049][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-06 16:05:33.049][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-06 16:05:33.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.055][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-06 16:05:33.092][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:33.107][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-06 16:05:33.108][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.109][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:05:33.110][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.111][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:05:33.111][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:33.112][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:05:33.113][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:05:33.114][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:05:33.115][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.116][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-06 16:05:33.117][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:05:33.118][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.119][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.119][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:05:33.119][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:05:33.119][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:05:33.119][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:05:33.119][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:05:33.120][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:05:33.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:33.122][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:33.123][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:05:33.124][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:33.124][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:33.125][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:05:33.126][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.127][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:05:33.128][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:05:33.129][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:33.130][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.131][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-06 16:05:33.132][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:33.133][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:05:33.134][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.135][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:05:33.136][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.137][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:05:33.137][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:33.138][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:05:33.139][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:05:33.140][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:05:33.141][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.142][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-06 16:05:33.143][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:05:33.144][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.145][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.145][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:05:33.145][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:05:33.145][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:05:33.145][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:05:33.145][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:05:33.146][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:05:33.147][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:33.148][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:33.149][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:05:33.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:33.150][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:33.151][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:05:33.152][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.153][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:05:33.154][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:05:33.155][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:33.155][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.157][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-06 16:05:33.158][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.159][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-06 16:05:33.160][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.161][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:05:33.162][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.162][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:05:33.163][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:33.164][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:05:33.165][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:05:33.166][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:05:33.167][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:33.168][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-06 16:05:33.169][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:05:33.170][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.170][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.171][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.172][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:05:33.173][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:33.174][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:33.175][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:05:33.175][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:33.176][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:33.177][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:05:33.178][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.179][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:05:33.180][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:05:33.180][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:33.181][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.182][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-06 16:05:33.184][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.185][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:05:33.186][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.187][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:05:33.187][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.188][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:05:33.189][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:33.190][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:05:33.191][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:05:33.192][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:05:33.193][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:33.194][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-06 16:05:33.194][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:05:33.195][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.196][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.197][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.198][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:05:33.199][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:33.200][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:33.200][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:05:33.201][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:33.202][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:33.203][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:05:33.204][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.205][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:05:33.205][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:05:33.206][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:33.207][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.211][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:05:33.212][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.283][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[2024-07-06 16:05:33.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.292][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-06 16:05:33.298][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-06 16:05:33.300][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-06 16:05:33.301][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-06 16:05:33.302][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-06 16:05:33.304][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-06 16:05:33.305][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-06 16:05:33.307][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-06 16:05:33.308][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-06 16:05:33.309][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-06 16:05:33.311][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-06 16:05:33.312][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-06 16:05:33.313][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-06 16:05:33.315][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-06 16:05:33.316][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-06 16:05:33.318][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-06 16:05:33.319][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-06 16:05:33.320][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-06 16:05:33.322][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-06 16:05:33.323][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-06 16:05:33.325][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-06 16:05:33.326][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-06 16:05:33.327][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-06 16:05:33.329][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-06 16:05:33.330][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-06 16:05:33.332][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-06 16:05:33.333][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-06 16:05:33.334][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-06 16:05:33.336][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-06 16:05:33.337][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-06 16:05:33.339][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-06 16:05:33.340][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-06 16:05:33.341][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-06 16:05:33.343][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-06 16:05:33.344][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-06 16:05:33.345][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-06 16:05:33.347][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-06 16:05:33.348][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-06 16:05:33.350][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-06 16:05:33.351][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-06 16:05:33.352][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-06 16:05:33.354][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-06 16:05:33.355][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-06 16:05:33.356][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-06 16:05:33.358][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-06 16:05:33.359][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-06 16:05:33.361][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-06 16:05:33.362][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-06 16:05:33.364][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-06 16:05:33.365][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-06 16:05:33.366][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-06 16:05:33.368][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-06 16:05:33.369][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-06 16:05:33.370][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-06 16:05:33.372][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-06 16:05:33.373][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-06 16:05:33.375][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-06 16:05:33.376][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-06 16:05:33.377][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-06 16:05:33.379][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-06 16:05:33.380][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-06 16:05:33.382][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-06 16:05:33.383][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-06 16:05:33.384][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-06 16:05:33.386][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-06 16:05:33.387][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-06 16:05:33.389][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-06 16:05:33.390][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-06 16:05:33.391][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-06 16:05:33.393][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-06 16:05:33.394][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-06 16:05:33.395][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-06 16:05:33.397][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-06 16:05:33.398][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-06 16:05:33.399][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-06 16:05:33.401][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-06 16:05:33.402][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-06 16:05:33.404][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-06 16:05:33.405][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-06 16:05:33.406][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-06 16:05:33.408][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-06 16:05:33.409][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-06 16:05:33.410][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-06 16:05:33.428][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-06 16:05:33.429][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:05:33.433][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:05:33.434][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.436][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:33.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:33.537][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-07-06 16:05:33.546][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-07-06 16:05:33.547][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:33.548][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-07-06 16:05:33.549][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.550][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:05:33.551][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:33.552][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-07-06 16:05:33.553][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.554][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:05:33.555][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-07-06 16:05:33.555][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:05:33.556][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.557][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-07-06 16:05:33.558][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:05:33.559][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-07-06 16:05:33.559][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-07-06 16:05:33.559][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-07-06 16:05:33.559][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-07-06 16:05:33.559][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-07-06 16:05:33.559][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-07-06 16:05:33.559][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-07-06 16:05:33.560][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:33.561][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.562][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-06 16:05:33.563][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:33.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:33.564][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:05:33.565][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:33.566][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:33.567][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:05:33.568][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-06 16:05:33.568][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-06 16:05:33.568][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-07-06 16:05:33.568][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-07-06 16:05:33.569][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:05:33.569][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:05:33.570][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:33.571][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:33.577][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-07-06 16:05:33.604][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-07-06 16:05:33.605][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-07-06 16:05:33.609][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-07-06 16:05:33.613][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-07-06 16:05:33.618][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:05:33.618][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:05:33.620][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-06 16:05:33.621][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-06 16:05:33.622][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-06 16:05:33.623][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-07-06 16:05:33.632][biodb::testThat]
biodb.INFO [2024-07-06 16:05:33.633][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-07-06 16:05:33.634][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:05:33.635][biodb::testThat]
biodb.TRACE[2024-07-06 16:05:33.638][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-07-06 16:05:33.640][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-07-06 16:05:33.644][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-07-06 16:05:33.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:05:33.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:33.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:33.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:33.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:33.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:33.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-06 16:05:33.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.704][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:33.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:33.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.731][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:33.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:33.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:33.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:33.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:33.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:33.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:33.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:33.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:33.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:33.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.751][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:33.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:33.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.754][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:33.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:33.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.758][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:33.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:33.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.762][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:33.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:33.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.806][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:33.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:33.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:05:33.861][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-07-06 16:05:33.863][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:05:33.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:05:33.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.867][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:05:33.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:05:33.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.870][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:05:33.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:05:33.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.874][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:05:33.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:05:33.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.905][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:33.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:33.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.939][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:33.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:33.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.943][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:33.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:33.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.946][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:33.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:33.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.967][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.967][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.969][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:33.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:33.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.980][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:33.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:33.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.984][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:33.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:33.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.988][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:33.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:33.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.991][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:33.992][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:33.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.994][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:33.995][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:33.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:33.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:33.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.005][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.015][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.016][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.018][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.033][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.040][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.041][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.042][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.043][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.053][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.057][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.068][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.069][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.070][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.071][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.081][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.082][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.084][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.088][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:34.089][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:34.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.090][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.094][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.095][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.097][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.100][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.101][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.103][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.107][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.108][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.109][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.124][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-07-06 16:05:34.156][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-07-06 16:05:34.157][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-07-06 16:05:34.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:05:34.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:34.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:34.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:34.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:34.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:34.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-06 16:05:34.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.203][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.207][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.211][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:34.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:34.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.215][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:34.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:34.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.226][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.230][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.233][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.237][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.240][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.244][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.247][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.259][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.267][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.271][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.278][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:05:34.303][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-07-06 16:05:34.326][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:05:34.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:05:34.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.329][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:05:34.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:05:34.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.333][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:05:34.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:05:34.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.336][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:05:34.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:05:34.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.348][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.377][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.381][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.385][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.413][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.414][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.416][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.426][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.430][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.438][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.441][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.442][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.444][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.445][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.461][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.465][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.466][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.468][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.468][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.478][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:34.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:34.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.482][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:34.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:34.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.485][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:34.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:34.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.489][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:34.490][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:34.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.491][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.492][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:34.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:34.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.512][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.513][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.515][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.526][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.536][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.537][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.539][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.540][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.564][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.565][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.567][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.578][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.578][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.580][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.584][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.585][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.587][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.590][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:34.591][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:34.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.593][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.597][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.598][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.599][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.603][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.604][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.605][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.609][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.610][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.612][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.615][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.616][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.618][ef$get] fields variable is a list.
biodb.INFO [2024-07-06 16:05:34.624][biodb::testThat]
biodb.INFO [2024-07-06 16:05:34.625][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-06 16:05:34.626][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:05:34.627][biodb::testThat]
biodb.DEBUG[2024-07-06 16:05:34.628][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-07-06 16:05:34.635][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-07-06 16:05:34.639][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2024-07-06 16:05:34.641][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2024-07-06 16:05:34.643][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-07-06 16:05:34.644][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-07-06 16:05:34.645][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2024-07-06 16:05:34.646][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-07-06 16:05:34.647][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-07-06 16:05:34.648][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-07-06 16:05:34.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:05:34.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:34.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:34.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:34.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:34.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:34.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-06 16:05:34.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.672][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:34.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:34.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.675][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:34.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:34.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.691][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.699][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.703][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.707][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.710][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.717][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:05:34.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:05:34.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:34.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:34.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:34.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:34.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:34.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-06 16:05:34.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.756][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.759][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:05:34.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.763][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:34.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:34.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.767][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:05:34.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:05:34.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:05:34.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:05:34.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:05:34.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:05:34.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:05:34.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.811][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.815][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:05:34.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.819][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.826][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.833][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:05:34.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:05:34.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:05:34.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:05:34.869][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-07-06 16:05:34.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-06 16:05:34.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-06 16:05:34.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:05:34.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:05:34.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:05:34.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:05:34.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-06 16:05:34.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-06 16:05:34.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:05:34.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:05:34.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:05:34.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:05:34.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-06 16:05:34.900][biodb::testThat]
biodb.INFO [2024-07-06 16:05:34.901][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-06 16:05:34.902][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:05:34.902][biodb::testThat]
biodb.INFO [2024-07-06 16:05:34.908][biodb::testThat]
biodb.INFO [2024-07-06 16:05:34.908][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-07-06 16:05:34.909][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:05:34.910][biodb::testThat]
biodb.WARN [2024-07-06 16:05:34.929][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-07-06 16:05:34.951][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-07-06 16:05:34.959][biodb::testThat]
biodb.INFO [2024-07-06 16:05:34.960][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-07-06 16:05:34.961][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:05:34.961][biodb::testThat]
biodb.TRACE[2024-07-06 16:05:34.982][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:05:34.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:05:34.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.986][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:05:34.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:05:34.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.990][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:05:34.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:05:34.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:34.993][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:05:34.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:05:34.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:34.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:35.026][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:05:35.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:05:35.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:35.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:35.030][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:05:35.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:05:35.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:35.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:35.033][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:05:35.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:05:35.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:35.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:05:35.037][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:05:35.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:05:35.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:05:35.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-06 16:05:35.045][biodb::testThat]
biodb.INFO [2024-07-06 16:05:35.046][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-06 16:05:35.046][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:05:35.047][biodb::testThat]
biodb.INFO [2024-07-06 16:05:35.053][biodb::testThat]
biodb.INFO [2024-07-06 16:05:35.054][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-06 16:05:35.055][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:05:35.056][biodb::testThat]
biodb.INFO [2024-07-06 16:05:35.066][biodb::testThat]
biodb.INFO [2024-07-06 16:05:35.067][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-06 16:05:35.068][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:05:35.069][biodb::testThat]
biodb.INFO [2024-07-06 16:05:35.074][biodb::testThat]
biodb.INFO [2024-07-06 16:05:35.075][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-06 16:05:35.076][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:05:35.076][biodb::testThat]
biodb.INFO [2024-07-06 16:05:35.081][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-06 16:05:35.082][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-07-06 16:05:35.083][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-07-06 16:05:35.084][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-06 16:05:35.085][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.086][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.088][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-06 16:05:35.097][biodb::testContext]
biodb.INFO [2024-07-06 16:05:35.098][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:05:35.099][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-07-06 16:05:35.100][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:05:35.101][biodb::testContext]
biodb.INFO [2024-07-06 16:05:35.102][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:05:35.104][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-06 16:05:35.107][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:05:35.108][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-06 16:05:35.109][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-06 16:05:35.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.112][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-06 16:05:35.113][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-06 16:05:35.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.117][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-06 16:05:35.118][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-06 16:05:35.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.121][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-06 16:05:35.122][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-06 16:05:35.123][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-06 16:05:35.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.126][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-06 16:05:35.127][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-06 16:05:35.128][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-06 16:05:35.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.131][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-06 16:05:35.132][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-06 16:05:35.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.135][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-06 16:05:35.136][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-06 16:05:35.137][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-06 16:05:35.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.140][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-06 16:05:35.141][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-06 16:05:35.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.144][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-06 16:05:35.145][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-06 16:05:35.146][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-06 16:05:35.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.149][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:05:35.150][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-06 16:05:35.151][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-06 16:05:35.152][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-06 16:05:35.153][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-06 16:05:35.154][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-06 16:05:35.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.157][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-06 16:05:35.158][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-06 16:05:35.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.161][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-06 16:05:35.162][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-06 16:05:35.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.165][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-06 16:05:35.166][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-06 16:05:35.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.169][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-06 16:05:35.170][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-06 16:05:35.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.174][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-06 16:05:35.175][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-06 16:05:35.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.178][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:05:35.179][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-06 16:05:35.182][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-06 16:05:35.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.185][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-06 16:05:35.191][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-06 16:05:35.192][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-06 16:05:35.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.195][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-06 16:05:35.197][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:35.198][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-06 16:05:35.199][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.199][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:05:35.200][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.201][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:05:35.202][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:35.203][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:05:35.204][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:05:35.205][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:05:35.206][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.207][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-06 16:05:35.208][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:05:35.209][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.209][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.210][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:05:35.210][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:05:35.210][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:05:35.210][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:05:35.210][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:05:35.211][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:05:35.212][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:35.213][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:35.214][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:05:35.215][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:35.215][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:35.216][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:05:35.217][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.218][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:05:35.219][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:05:35.220][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:35.221][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.222][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-06 16:05:35.223][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:35.224][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:05:35.225][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.226][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:05:35.227][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.228][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:05:35.229][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:35.230][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:05:35.230][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:05:35.231][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:05:35.232][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.233][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-06 16:05:35.234][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:05:35.235][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.236][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.237][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:05:35.237][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:05:35.237][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:05:35.237][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:05:35.237][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:05:35.238][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:05:35.238][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:35.239][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:35.240][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:05:35.241][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:35.242][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:35.243][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:05:35.243][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.244][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:05:35.245][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:05:35.246][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:35.247][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.248][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-06 16:05:35.249][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.250][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-06 16:05:35.251][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.252][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:05:35.253][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.254][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:05:35.255][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:35.256][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:05:35.257][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:05:35.257][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:05:35.258][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:35.259][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-06 16:05:35.260][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:05:35.261][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.262][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.263][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.264][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:05:35.265][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:35.265][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:35.266][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:05:35.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:35.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:35.269][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:05:35.270][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.270][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:05:35.271][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:05:35.272][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:35.273][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.274][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-06 16:05:35.276][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.276][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:05:35.277][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.278][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:05:35.279][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.280][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:05:35.281][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:35.282][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:05:35.283][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:05:35.284][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:05:35.284][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:35.285][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-06 16:05:35.286][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:05:35.287][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.288][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.289][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.290][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:05:35.291][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:35.291][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:35.292][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:05:35.293][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:35.294][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:35.295][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:05:35.296][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.296][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:05:35.297][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:05:35.298][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:35.299][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.300][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:05:35.301][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.314][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[2024-07-06 16:05:35.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.329][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[2024-07-06 16:05:35.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.337][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[2024-07-06 16:05:35.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.361][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[2024-07-06 16:05:35.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.373][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-06 16:05:35.375][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-06 16:05:35.376][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-06 16:05:35.377][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-06 16:05:35.378][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-06 16:05:35.380][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-06 16:05:35.381][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-06 16:05:35.382][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-06 16:05:35.383][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-06 16:05:35.385][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-06 16:05:35.386][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-06 16:05:35.387][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-06 16:05:35.388][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-06 16:05:35.390][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-06 16:05:35.391][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-06 16:05:35.392][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-06 16:05:35.393][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-06 16:05:35.395][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-06 16:05:35.396][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-06 16:05:35.397][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-06 16:05:35.398][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-06 16:05:35.399][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-06 16:05:35.401][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-06 16:05:35.402][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-06 16:05:35.403][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-06 16:05:35.404][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-06 16:05:35.406][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-06 16:05:35.407][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-06 16:05:35.408][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-06 16:05:35.409][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-06 16:05:35.411][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-06 16:05:35.412][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-06 16:05:35.413][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-06 16:05:35.414][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-06 16:05:35.416][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-06 16:05:35.417][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-06 16:05:35.418][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-06 16:05:35.419][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-06 16:05:35.420][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-06 16:05:35.422][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-06 16:05:35.423][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-06 16:05:35.424][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-06 16:05:35.429][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-06 16:05:35.431][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-06 16:05:35.432][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-06 16:05:35.433][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-06 16:05:35.434][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-06 16:05:35.436][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-06 16:05:35.437][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-06 16:05:35.438][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-06 16:05:35.439][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-06 16:05:35.440][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-06 16:05:35.442][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-06 16:05:35.443][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-06 16:05:35.444][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-06 16:05:35.445][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-06 16:05:35.447][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-06 16:05:35.448][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-06 16:05:35.449][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-06 16:05:35.450][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-06 16:05:35.452][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-06 16:05:35.453][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-06 16:05:35.454][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-06 16:05:35.455][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-06 16:05:35.457][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-06 16:05:35.458][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-06 16:05:35.459][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-06 16:05:35.460][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-06 16:05:35.461][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-06 16:05:35.463][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-06 16:05:35.464][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-06 16:05:35.465][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-06 16:05:35.466][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-06 16:05:35.468][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-06 16:05:35.469][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-06 16:05:35.470][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-06 16:05:35.471][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-06 16:05:35.473][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-06 16:05:35.474][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-06 16:05:35.475][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-06 16:05:35.476][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-06 16:05:35.478][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-06 16:05:35.479][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-06 16:05:35.480][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-06 16:05:35.482][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:05:35.483][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:05:35.483][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.485][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:05:35.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:05:35.585][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-07-06 16:05:35.586][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-07-06 16:05:35.588][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:35.589][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-07-06 16:05:35.590][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.591][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:05:35.591][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:35.592][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-07-06 16:05:35.593][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.594][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:05:35.595][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-07-06 16:05:35.596][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:05:35.597][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.598][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-07-06 16:05:35.599][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:05:35.599][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-07-06 16:05:35.599][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-07-06 16:05:35.599][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-07-06 16:05:35.599][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-07-06 16:05:35.599][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-07-06 16:05:35.599][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-07-06 16:05:35.599][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-07-06 16:05:35.600][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-06 16:05:35.601][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.602][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-06 16:05:35.603][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:35.604][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:35.605][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:05:35.606][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:05:35.606][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:05:35.607][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:05:35.608][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-06 16:05:35.608][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-06 16:05:35.608][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-07-06 16:05:35.608][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-07-06 16:05:35.609][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:05:35.610][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:05:35.611][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-06 16:05:35.612][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:05:35.613][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-07-06 16:05:35.616][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-07-06 16:05:35.616][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-07-06 16:05:35.618][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-07-06 16:05:35.619][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-07-06 16:05:35.620][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:05:35.621][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:05:35.622][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-06 16:05:35.623][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-06 16:05:35.624][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-06 16:05:35.625][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-07-06 16:05:35.626][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-06 16:05:35.627][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-07-06 16:05:35.628][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-07-06 16:05:35.629][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-06 16:05:35.630][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:05:35.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:05:35.631][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:05:35.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:05:35.633][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:05:35.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  4.233   0.183   4.405 

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* 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 ‘1.9.0’
* 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
* 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 loading without being on the library search path ... 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.


Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-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)