Back to Long Tests report for BioC 3.19

This page was generated on 2024-06-08 23:55 -0400 (Sat, 08 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 12/33HostnameOS / ArchCHECK
biodbNci 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-08 09:55 -0400 (Sat, 08 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_19
git_last_commit: 0db4525
git_last_commit_date: 2024-04-30 11:41:04 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbNci on nebbiolo1

To the developers/maintainers of the biodbNci package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbNci
Version: 1.8.0
Command: /home/biocbuild/bbs-3.19-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_1.8.0.tar.gz
StartedAt: 2024-06-08 16:05:50 -0400 (Sat, 08 Jun 2024)
EndedAt: 2024-06-08 16:06:54 -0400 (Sat, 08 Jun 2024)
EllapsedTime: 64.1 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 [2024-06-08 16:06:50.671][biodb::testContext]
biodb.INFO [2024-06-08 16:06:50.673][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:06:50.674][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-08 16:06:50.675][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:06:50.676][biodb::testContext]
biodb.INFO [2024-06-08 16:06:50.682][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-08 16:06:50.684][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-08 16:06:50.691][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:06:50.692][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-08 16:06:50.693][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-08 16:06:50.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.696][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-08 16:06:50.713][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-08 16:06:50.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.716][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-08 16:06:50.717][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-08 16:06:50.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.720][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-08 16:06:50.721][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-08 16:06:50.722][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-08 16:06:50.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.725][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-08 16:06:50.726][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-08 16:06:50.727][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-08 16:06:50.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.730][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-08 16:06:50.731][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-08 16:06:50.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.734][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-08 16:06:50.735][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-08 16:06:50.736][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-08 16:06:50.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.739][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-08 16:06:50.740][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-08 16:06:50.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.744][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-08 16:06:50.745][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-08 16:06:50.745][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-08 16:06:50.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.749][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:06:50.750][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-08 16:06:50.751][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-08 16:06:50.751][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-08 16:06:50.752][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-08 16:06:50.753][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-08 16:06:50.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.757][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-08 16:06:50.757][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-08 16:06:50.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.761][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-08 16:06:50.762][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-08 16:06:50.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.765][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-08 16:06:50.766][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-08 16:06:50.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.769][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-08 16:06:50.770][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-08 16:06:50.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.773][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-08 16:06:50.774][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-08 16:06:50.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.778][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:06:50.778][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-08 16:06:50.782][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-08 16:06:50.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.785][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-08 16:06:50.786][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-08 16:06:50.787][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-08 16:06:50.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.793][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-08 16:06:50.828][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:50.841][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-08 16:06:50.842][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.843][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:06:50.844][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.845][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:06:50.846][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:50.847][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:06:50.848][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:06:50.849][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:06:50.849][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.850][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-08 16:06:50.851][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:06:50.852][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:50.853][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.854][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:06:50.854][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:06:50.854][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:06:50.854][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:06:50.854][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:06:50.855][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:06:50.856][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:50.857][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:50.857][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:06:50.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:50.859][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:50.860][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:06:50.861][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:50.862][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:06:50.862][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:06:50.863][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:50.864][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:50.865][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-08 16:06:50.867][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:50.868][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:06:50.869][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.869][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:06:50.870][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.871][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:06:50.872][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:50.873][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:06:50.874][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:06:50.875][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:06:50.876][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.877][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-08 16:06:50.877][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:06:50.878][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:50.879][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.880][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:06:50.880][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:06:50.880][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:06:50.880][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:06:50.880][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:06:50.881][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:06:50.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:50.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:50.884][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:06:50.884][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:50.885][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:50.886][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:06:50.887][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:50.888][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:06:50.889][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:06:50.890][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:50.890][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:50.891][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-08 16:06:50.893][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.894][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-08 16:06:50.895][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.896][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:06:50.897][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.897][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:06:50.898][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:50.899][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:06:50.900][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:06:50.901][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:06:50.902][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:50.903][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-08 16:06:50.904][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:06:50.905][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:50.905][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.906][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:50.907][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:06:50.908][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:50.909][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:50.910][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:06:50.911][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:50.911][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:50.912][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:06:50.913][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:50.914][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:06:50.915][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:06:50.916][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:50.917][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:50.918][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-08 16:06:50.919][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.920][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:06:50.921][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.922][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:06:50.923][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.924][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:06:50.924][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:50.925][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:06:50.926][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:06:50.927][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:06:50.928][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:50.929][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-08 16:06:50.930][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:06:50.931][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:50.932][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:50.932][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:50.933][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:06:50.934][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:50.935][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:50.936][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:06:50.937][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:50.938][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:50.938][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:06:50.939][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:50.940][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:06:50.941][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:06:50.942][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:50.943][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:50.946][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:06:50.947][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:50.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:50.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:50.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:50.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:50.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:50.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:50.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:50.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:50.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:50.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:50.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:50.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:50.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:50.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:50.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:50.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.983][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[2024-06-08 16:06:50.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:50.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:50.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:50.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:50.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:50.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:50.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:50.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:50.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:50.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:50.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:50.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.011][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[2024-06-08 16:06:51.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.019][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[2024-06-08 16:06:51.020][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-08 16:06:51.024][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-08 16:06:51.025][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-08 16:06:51.027][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-08 16:06:51.028][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-08 16:06:51.029][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-08 16:06:51.030][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-08 16:06:51.032][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-08 16:06:51.033][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-08 16:06:51.034][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-08 16:06:51.035][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-08 16:06:51.037][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-08 16:06:51.038][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-08 16:06:51.039][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-08 16:06:51.040][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-08 16:06:51.042][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-08 16:06:51.043][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-08 16:06:51.044][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-08 16:06:51.045][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-08 16:06:51.047][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-08 16:06:51.048][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-08 16:06:51.049][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-08 16:06:51.050][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-08 16:06:51.052][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-08 16:06:51.053][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-08 16:06:51.054][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-08 16:06:51.055][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-08 16:06:51.057][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-08 16:06:51.058][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-08 16:06:51.059][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-08 16:06:51.060][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-08 16:06:51.062][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-08 16:06:51.063][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-08 16:06:51.064][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-08 16:06:51.065][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-08 16:06:51.066][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-08 16:06:51.068][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-08 16:06:51.069][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-08 16:06:51.070][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-08 16:06:51.071][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-08 16:06:51.073][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-08 16:06:51.074][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-08 16:06:51.075][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-08 16:06:51.076][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-08 16:06:51.078][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-08 16:06:51.083][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-08 16:06:51.085][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-08 16:06:51.086][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-08 16:06:51.087][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-08 16:06:51.089][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-08 16:06:51.090][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-08 16:06:51.092][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-08 16:06:51.093][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-08 16:06:51.095][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-08 16:06:51.096][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-08 16:06:51.097][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-08 16:06:51.099][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-08 16:06:51.100][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-08 16:06:51.102][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-08 16:06:51.103][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-08 16:06:51.104][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-08 16:06:51.106][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-08 16:06:51.107][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-08 16:06:51.109][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-08 16:06:51.110][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-08 16:06:51.111][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-08 16:06:51.113][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-08 16:06:51.114][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-08 16:06:51.116][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-08 16:06:51.117][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-08 16:06:51.118][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-08 16:06:51.120][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-08 16:06:51.121][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-08 16:06:51.122][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-08 16:06:51.124][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-08 16:06:51.125][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-08 16:06:51.126][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-08 16:06:51.128][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-08 16:06:51.129][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-08 16:06:51.131][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-08 16:06:51.132][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-08 16:06:51.133][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-08 16:06:51.135][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-08 16:06:51.141][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-08 16:06:51.143][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-08 16:06:51.147][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:06:51.147][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.149][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.185][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[2024-06-08 16:06:51.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:51.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:51.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.269][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[2024-06-08 16:06:51.270][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-06-08 16:06:51.279][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-06-08 16:06:51.280][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:51.281][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-06-08 16:06:51.282][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:51.283][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:06:51.284][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:51.285][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-06-08 16:06:51.286][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:51.287][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:06:51.288][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-06-08 16:06:51.289][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:06:51.289][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:51.290][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-06-08 16:06:51.291][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:06:51.292][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-06-08 16:06:51.292][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-06-08 16:06:51.292][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-06-08 16:06:51.292][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-06-08 16:06:51.292][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-06-08 16:06:51.292][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-06-08 16:06:51.292][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-06-08 16:06:51.293][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:51.294][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:51.295][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-08 16:06:51.296][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:51.297][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:51.298][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:06:51.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:51.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:51.300][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:06:51.301][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-08 16:06:51.301][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-08 16:06:51.301][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-06-08 16:06:51.301][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-06-08 16:06:51.302][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:06:51.303][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:06:51.304][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:51.304][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:51.310][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-06-08 16:06:51.331][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-06-08 16:06:51.336][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-06-08 16:06:51.340][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-06-08 16:06:51.344][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-06-08 16:06:51.348][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:06:51.349][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:06:51.350][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:06:51.351][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:06:51.352][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:06:51.353][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-06-08 16:06:51.362][biodb::testThat]
biodb.INFO [2024-06-08 16:06:51.363][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-08 16:06:51.364][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:06:51.365][biodb::testThat]
biodb.TRACE[2024-06-08 16:06:51.368][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-06-08 16:06:51.370][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-06-08 16:06:51.373][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-06-08 16:06:51.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:06:51.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:06:51.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.432][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:51.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:51.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.457][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:51.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:51.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:51.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:51.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:51.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:51.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.480][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.484][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.488][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.495][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:06:51.582][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-06-08 16:06:51.584][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:06:51.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:06:51.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.587][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:06:51.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:06:51.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.591][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:06:51.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:06:51.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.595][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:06:51.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:06:51.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.625][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.658][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.662][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.665][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.685][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.686][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.688][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.699][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:51.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:51.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.702][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:51.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:51.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.706][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:51.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:51.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.709][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:51.710][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:51.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.712][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.713][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:51.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:51.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.729][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.733][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.734][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.736][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.746][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:51.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:51.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:51.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:51.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:51.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:51.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.757][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:51.758][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:51.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.759][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.760][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:51.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:51.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.770][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.773][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.780][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.781][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.786][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.796][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.797][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.799][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.803][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:51.803][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:51.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.805][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.809][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:51.810][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:51.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.811][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.815][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.816][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.818][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.821][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.822][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.824][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.838][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-06-08 16:06:51.869][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-06-08 16:06:51.870][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-06-08 16:06:51.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:06:51.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:51.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:51.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:51.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:51.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:51.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:06:51.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.913][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:06:51.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:06:51.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.917][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:06:51.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:06:51.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.921][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:51.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:51.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.924][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:51.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:51.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:51.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.936][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:51.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:51.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.939][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:51.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:51.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.943][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:51.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:51.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.946][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:51.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:51.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:51.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:51.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:51.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:51.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:51.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:51.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.961][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:51.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:51.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.965][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:51.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:51.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:51.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.976][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.980][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.987][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:51.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:51.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:51.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:51.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:51.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:06:52.012][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-06-08 16:06:52.033][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:06:52.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:06:52.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.036][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:06:52.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:06:52.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.040][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:06:52.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:06:52.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.043][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:06:52.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:06:52.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.054][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.083][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.086][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.090][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.117][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.118][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.120][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.130][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.134][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.137][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.141][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.142][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.143][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.143][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.144][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:52.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:52.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:52.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:52.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:52.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:52.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.167][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:52.168][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:52.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.170][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.171][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:52.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:52.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.180][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:52.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:52.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.184][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:52.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:52.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.187][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:52.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:52.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.191][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:52.192][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:52.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.194][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.195][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:52.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:52.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.211][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.215][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.215][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.217][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.227][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:52.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:52.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:52.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:52.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.234][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:52.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:52.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.238][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:52.239][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:52.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.241][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:52.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:52.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.258][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.261][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.262][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.264][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.265][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.277][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.278][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.280][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.283][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.284][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.286][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.290][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:52.290][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:52.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.292][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.296][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:52.297][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:52.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.298][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.302][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.303][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.304][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.308][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.309][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.311][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.314][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:52.315][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:52.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.317][ef$get] fields variable is a list.
biodb.INFO [2024-06-08 16:06:52.323][biodb::testThat]
biodb.INFO [2024-06-08 16:06:52.324][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-08 16:06:52.324][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:06:52.325][biodb::testThat]
biodb.DEBUG[2024-06-08 16:06:52.327][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-06-08 16:06:52.334][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-06-08 16:06:52.338][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2024-06-08 16:06:52.340][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2024-06-08 16:06:52.341][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-06-08 16:06:52.342][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-06-08 16:06:52.344][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[2024-06-08 16:06:52.345][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-06-08 16:06:52.346][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-06-08 16:06:52.347][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-06-08 16:06:52.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:06:52.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:52.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:52.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:52.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:52.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:06:52.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.370][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:52.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:52.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.374][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:52.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:52.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.385][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:52.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:52.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.389][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:52.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:52.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.393][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.396][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.400][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.404][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.415][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:06:52.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:06:52.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:52.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:52.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:52.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:52.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:06:52.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.453][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.456][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:06:52.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.460][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:52.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:52.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.464][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:06:52.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:06:52.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:06:52.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:52.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:52.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.479][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:52.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:52.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:52.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:52.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.486][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:52.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:52.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.489][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:52.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:52.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:52.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:52.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.496][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:52.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:52.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.501][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:52.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:52.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.504][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:06:52.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:06:52.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.508][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:06:52.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.516][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.519][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.527][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:06:52.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:06:52.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:06:52.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:06:52.566][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-06-08 16:06:52.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-08 16:06:52.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-08 16:06:52.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:06:52.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:06:52.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:06:52.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:06:52.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-08 16:06:52.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-08 16:06:52.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:06:52.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:06:52.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:06:52.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:06:52.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-08 16:06:52.596][biodb::testThat]
biodb.INFO [2024-06-08 16:06:52.597][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-08 16:06:52.598][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:06:52.599][biodb::testThat]
biodb.INFO [2024-06-08 16:06:52.604][biodb::testThat]
biodb.INFO [2024-06-08 16:06:52.605][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-08 16:06:52.606][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:06:52.606][biodb::testThat]
biodb.WARN [2024-06-08 16:06:52.625][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-06-08 16:06:52.642][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-06-08 16:06:52.649][biodb::testThat]
biodb.INFO [2024-06-08 16:06:52.650][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-08 16:06:52.651][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:06:52.652][biodb::testThat]
biodb.TRACE[2024-06-08 16:06:52.675][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:06:52.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:06:52.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.679][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:06:52.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:06:52.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.682][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:06:52.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:06:52.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.686][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:06:52.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:06:52.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.718][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:06:52.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:06:52.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.721][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:06:52.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:06:52.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.725][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:06:52.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:06:52.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:52.729][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:06:52.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:06:52.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:52.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-08 16:06:52.736][biodb::testThat]
biodb.INFO [2024-06-08 16:06:52.737][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-08 16:06:52.738][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:06:52.739][biodb::testThat]
biodb.INFO [2024-06-08 16:06:52.744][biodb::testThat]
biodb.INFO [2024-06-08 16:06:52.745][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-08 16:06:52.746][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:06:52.747][biodb::testThat]
biodb.INFO [2024-06-08 16:06:52.753][biodb::testThat]
biodb.INFO [2024-06-08 16:06:52.754][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-08 16:06:52.754][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:06:52.755][biodb::testThat]
biodb.INFO [2024-06-08 16:06:52.760][biodb::testThat]
biodb.INFO [2024-06-08 16:06:52.761][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-08 16:06:52.762][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:06:52.763][biodb::testThat]
biodb.INFO [2024-06-08 16:06:52.767][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-08 16:06:52.772][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-06-08 16:06:52.773][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-06-08 16:06:52.773][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-08 16:06:52.774][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:52.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:52.776][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:52.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:52.777][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-08 16:06:52.786][biodb::testContext]
biodb.INFO [2024-06-08 16:06:52.787][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:06:52.788][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-08 16:06:52.789][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:06:52.789][biodb::testContext]
biodb.INFO [2024-06-08 16:06:52.791][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-08 16:06:52.793][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-08 16:06:52.796][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:06:52.797][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-08 16:06:52.798][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-08 16:06:52.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.801][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-08 16:06:52.802][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-08 16:06:52.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.805][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-08 16:06:52.806][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-08 16:06:52.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.810][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-08 16:06:52.810][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-08 16:06:52.811][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-08 16:06:52.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.815][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-08 16:06:52.816][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-08 16:06:52.817][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-08 16:06:52.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.820][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-08 16:06:52.821][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-08 16:06:52.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.824][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-08 16:06:52.825][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-08 16:06:52.826][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-08 16:06:52.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.829][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-08 16:06:52.830][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-08 16:06:52.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.833][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-08 16:06:52.834][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-08 16:06:52.835][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-08 16:06:52.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.838][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:06:52.839][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-08 16:06:52.840][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-08 16:06:52.841][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-08 16:06:52.842][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-08 16:06:52.843][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-08 16:06:52.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.846][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-08 16:06:52.847][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-08 16:06:52.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.850][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-08 16:06:52.851][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-08 16:06:52.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.854][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-08 16:06:52.855][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-08 16:06:52.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.859][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-08 16:06:52.860][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-08 16:06:52.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.863][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-08 16:06:52.864][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-08 16:06:52.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.867][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:06:52.868][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-08 16:06:52.871][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-08 16:06:52.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.874][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-08 16:06:52.875][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-08 16:06:52.876][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-08 16:06:52.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.879][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-08 16:06:52.881][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:52.882][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-08 16:06:52.883][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.883][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:06:52.884][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.885][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:06:52.886][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:52.887][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:06:52.888][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:06:52.889][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:06:52.890][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.891][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-08 16:06:52.891][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:06:52.896][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:52.897][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.898][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:06:52.898][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:06:52.898][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:06:52.898][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:06:52.898][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:06:52.898][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:06:52.899][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:52.900][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:52.901][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:06:52.902][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:52.903][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:52.903][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:06:52.904][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:52.905][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:06:52.906][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:06:52.907][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:52.908][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:52.909][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-08 16:06:52.910][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:52.911][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:06:52.912][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.913][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:06:52.914][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.915][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:06:52.916][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:52.917][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:06:52.917][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:06:52.918][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:06:52.919][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.920][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-08 16:06:52.921][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:06:52.922][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:52.923][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.924][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:06:52.924][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:06:52.924][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:06:52.924][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:06:52.924][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:06:52.925][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:06:52.926][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:52.926][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:52.927][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:06:52.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:52.929][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:52.930][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:06:52.931][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:52.931][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:06:52.932][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:06:52.933][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:52.934][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:52.935][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-08 16:06:52.937][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.938][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-08 16:06:52.938][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.939][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:06:52.940][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.941][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:06:52.942][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:52.943][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:06:52.944][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:06:52.945][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:06:52.946][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:52.946][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-08 16:06:52.947][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:06:52.948][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:52.949][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.950][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:52.951][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:06:52.952][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:52.953][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:52.953][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:06:52.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:52.955][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:52.956][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:06:52.957][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:52.958][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:06:52.958][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:06:52.959][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:52.960][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:52.961][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-08 16:06:52.963][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.964][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:06:52.965][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.965][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:06:52.966][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.967][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:06:52.968][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:52.969][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:06:52.970][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:06:52.971][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:06:52.972][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:52.973][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-08 16:06:52.974][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:06:52.974][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:52.975][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:52.976][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:52.977][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:06:52.978][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:52.979][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:52.980][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:06:52.980][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:52.981][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:52.982][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:06:52.983][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:52.984][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:06:52.985][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:06:52.986][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:52.986][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:52.988][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:06:52.988][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:52.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:52.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.993][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[2024-06-08 16:06:52.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:52.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:52.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:52.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:52.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:52.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.052][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[2024-06-08 16:06:53.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.061][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-08 16:06:53.062][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-08 16:06:53.063][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-08 16:06:53.064][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-08 16:06:53.066][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-08 16:06:53.067][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-08 16:06:53.068][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-08 16:06:53.069][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-08 16:06:53.071][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-08 16:06:53.072][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-08 16:06:53.073][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-08 16:06:53.074][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-08 16:06:53.076][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-08 16:06:53.077][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-08 16:06:53.078][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-08 16:06:53.079][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-08 16:06:53.081][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-08 16:06:53.082][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-08 16:06:53.083][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-08 16:06:53.084][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-08 16:06:53.086][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-08 16:06:53.087][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-08 16:06:53.088][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-08 16:06:53.089][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-08 16:06:53.091][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-08 16:06:53.092][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-08 16:06:53.093][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-08 16:06:53.094][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-08 16:06:53.095][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-08 16:06:53.097][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-08 16:06:53.098][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-08 16:06:53.099][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-08 16:06:53.100][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-08 16:06:53.102][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-08 16:06:53.103][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-08 16:06:53.104][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-08 16:06:53.105][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-08 16:06:53.107][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-08 16:06:53.108][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-08 16:06:53.109][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-08 16:06:53.110][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-08 16:06:53.112][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-08 16:06:53.113][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-08 16:06:53.114][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-08 16:06:53.115][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-08 16:06:53.117][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-08 16:06:53.118][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-08 16:06:53.119][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-08 16:06:53.120][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-08 16:06:53.121][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-08 16:06:53.123][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-08 16:06:53.124][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-08 16:06:53.125][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-08 16:06:53.126][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-08 16:06:53.128][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-08 16:06:53.129][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-08 16:06:53.130][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-08 16:06:53.131][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-08 16:06:53.136][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-08 16:06:53.137][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-08 16:06:53.138][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-08 16:06:53.140][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-08 16:06:53.141][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-08 16:06:53.142][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-08 16:06:53.143][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-08 16:06:53.144][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-08 16:06:53.146][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-08 16:06:53.147][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-08 16:06:53.148][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-08 16:06:53.149][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-08 16:06:53.150][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-08 16:06:53.152][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-08 16:06:53.153][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-08 16:06:53.154][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-08 16:06:53.155][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-08 16:06:53.157][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-08 16:06:53.158][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-08 16:06:53.159][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-08 16:06:53.160][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-08 16:06:53.162][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-08 16:06:53.163][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-08 16:06:53.164][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-08 16:06:53.165][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-08 16:06:53.167][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-08 16:06:53.168][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-08 16:06:53.169][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:06:53.170][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.171][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.194][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[2024-06-08 16:06:53.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.228][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[2024-06-08 16:06:53.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.244][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[2024-06-08 16:06:53.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.259][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[2024-06-08 16:06:53.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:53.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:53.271][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-06-08 16:06:53.272][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-06-08 16:06:53.274][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:53.275][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-06-08 16:06:53.276][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:53.277][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:06:53.278][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:53.278][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-06-08 16:06:53.279][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:53.280][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:06:53.281][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-06-08 16:06:53.282][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:06:53.283][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:53.284][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-06-08 16:06:53.285][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:06:53.286][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-06-08 16:06:53.286][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-06-08 16:06:53.286][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-06-08 16:06:53.286][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-06-08 16:06:53.286][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-06-08 16:06:53.286][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-06-08 16:06:53.286][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-06-08 16:06:53.287][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:53.287][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:53.288][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-08 16:06:53.289][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:53.290][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:53.291][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:06:53.292][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:53.293][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:53.293][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:06:53.294][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-08 16:06:53.294][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-08 16:06:53.294][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-06-08 16:06:53.294][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-06-08 16:06:53.295][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:06:53.296][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:06:53.297][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:53.298][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:53.299][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-06-08 16:06:53.302][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-06-08 16:06:53.302][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-06-08 16:06:53.303][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-06-08 16:06:53.305][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-06-08 16:06:53.306][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:06:53.307][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:06:53.308][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:06:53.309][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:06:53.310][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:06:53.311][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-06-08 16:06:53.312][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-08 16:06:53.313][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-06-08 16:06:53.314][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-06-08 16:06:53.315][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-08 16:06:53.315][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:53.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:53.317][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:53.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:53.318][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:53.319][FUN] Functions in observer 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 
  4.067   0.215   4.272

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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: OK

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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-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-3.19-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-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)