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Testing of Ontology Grammar Wizard

John J. Camilleri
20 Aug 2012

Documentation

The template file format needs some sort of proper specification. The example available at resources/template.xml is OK, but it needs some instructions to accompany it.

Testing various SPARQL EndPoint URLs

So far I have not been able to get the SPARQL endpoint running locally on my machine. So, I have tested the plugin with publicly available endpoints found here: http://labs.mondeca.com/sparqlEndpointsStatus/. I selected various endpoint URLs at random and tested them with the Ontology Grammar Wizard. The results are below.

(local)

http://localhost:8080/repositories/molto-repository (no local server running): Connection refused

http://localhost:8080/molto-repository (server is running): Uncaught exception:

!ENTRY org.eclipse.ui 4 0 2012-08-20 13:10:00.909
!MESSAGE Unhandled event loop exception
!STACK 0
java.lang.IllegalStateException: Server URL has not been set
    at org.openrdf.http.client.HTTPClient.checkServerURL(HTTPClient.java:186)
    at org.openrdf.http.client.HTTPClient.setUsernameAndPassword(HTTPClient.java:300)
    at org.openrdf.repository.http.HTTPRepository.setUsernameAndPassword(HTTPRepository.java:211)
    at com.ontotext.molto.repositoryHelper.RepositoryUtils.<init>(RepositoryUtils.java:32)
    at org.grammaticalframework.eclipse.ontologygrammar.GFOntologyGrammarURLAndTemplatePage.validateURLField(GFOntologyGrammarURLAndTemplatePage.java:221)
    at org.grammaticalframework.eclipse.ontologygrammar.GFOntologyGrammarURLAndTemplatePage.access$0(GFOntologyGrammarURLAndTemplatePage.java:199)
    at org.grammaticalframework.eclipse.ontologygrammar.GFOntologyGrammarURLAndTemplatePage$1.widgetSelected(GFOntologyGrammarURLAndTemplatePage.java:122)
    at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:240)
    at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1258)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:3588)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3209)
    at org.eclipse.jface.window.Window.runEventLoop(Window.java:825)
    at org.eclipse.jface.window.Window.open(Window.java:801)
    at org.eclipse.ui.internal.handlers.WizardHandler$New.executeHandler(WizardHandler.java:257)
    at org.eclipse.ui.internal.handlers.WizardHandler.execute(WizardHandler.java:277)
    at org.eclipse.ui.internal.handlers.HandlerProxy.execute(HandlerProxy.java:293)
    at org.eclipse.core.commands.Command.executeWithChecks(Command.java:476)
    at org.eclipse.core.commands.ParameterizedCommand.executeWithChecks(ParameterizedCommand.java:508)
    at org.eclipse.ui.internal.handlers.HandlerService.executeCommand(HandlerService.java:169)
    at org.eclipse.ui.internal.handlers.SlaveHandlerService.executeCommand(SlaveHandlerService.java:241)
    at org.eclipse.ui.internal.actions.CommandAction.runWithEvent(CommandAction.java:157)
    at org.eclipse.ui.internal.actions.CommandAction.run(CommandAction.java:171)
    at org.eclipse.ui.actions.NewWizardDropDownAction.run(NewWizardDropDownAction.java:182)
    at org.eclipse.jface.action.Action.runWithEvent(Action.java:498)
    at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:584)
    at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:501)
    at org.eclipse.jface.action.ActionContributionItem$6.handleEvent(ActionContributionItem.java:452)
    at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1258)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:3588)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3209)
    at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2696)
    at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2660)
    at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2494)
    at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:674)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
    at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:667)
    at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
    at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:123)
    at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:616)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
    at org.eclipse.equinox.launcher.Main.main(Main.java:1386)

BBC Music

http://api.talis.com/stores/bbc-backstage/services/sparql Remote service returned an error

British National Bibliography (BNB) - Linked Open Data

http://bnb.data.bl.uk/sparql Remote service returned an error

CTIC Public Dataset Catalogs

http://data.fundacionctic.org/sparql 37000 Error SP030: SPARQL compiler, line 1: syntax error at 'group_concat' before '('

DPpedia in German

http://de.dbpedia.org/sparql Virtuoso 37000 Error SP030: SPARQL compiler, line 1: syntax error at 'group_concat' before '('

EEA Reporting Obligations Database

http://cr.eionet.europa.eu/sparql [Fatal Error] :1:1: Premature end of file.

European Employment Services (EURES)

http://www4.wiwiss.fu-berlin.de/eures/sparql Error returned as HTML document:

376377 [main] WARN  org.openrdf.http.client.HTTPClient  - Server reports problem: <html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"/>
<title>Error 400 Parse error: 
PREFIX ptop: &lt;http://proton.semanticweb.org/protontop#&gt;PREFIX owl: &lt;http://www.w3.org/2002/07/owl#&gt;PREFIX rdf: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;SELECT ?class (group_concat(?class_label;separator = ' ; ') as ?cnc){ ?class a owl:Class . ?class rdf:label ?class_label . FILTER (!isBlank(?class)) .} group by ?class

Encountered " "group" "group "" at line 1, column 166.
Was expecting one of:
    &lt;IRIref&gt; ...
    &lt;PNAME_NS&gt; ...
    &lt;PNAME_LN&gt; ...

IEEE Papers (RKBExplorer)

http://ieee.rkbexplorer.com/sparql/ Exception while connecting:

!SESSION 2012-08-20 09:15:58.974 -----------------------------------------------
eclipse.buildId=M20110909-1335
java.version=1.6.0_24
java.vendor=Sun Microsystems Inc.
BootLoader constants: OS=linux, ARCH=x86, WS=gtk, NL=en_GB
Framework arguments:  -product org.eclipse.sdk.ide
Command-line arguments:  -product org.eclipse.sdk.ide -data /home/john/repositories/gf-eclipse-plugin/workspace/../workspace-demo -dev file:/home/john/repositories/gf-eclipse-plugin/workspace/.metadata/.plugins/org.eclipse.pde.core/Eclipse Application/dev.properties -os linux -ws gtk -arch x86 -consoleLog

!ENTRY org.eclipse.ui 4 0 2012-08-20 09:27:49.504
!MESSAGE Unhandled event loop exception
!STACK 0
java.lang.NullPointerException
    at org.openrdf.query.impl.TupleQueryResultImpl.<init>(TupleQueryResultImpl.java:48)
    at org.openrdf.query.impl.TupleQueryResultBuilder.getQueryResult(TupleQueryResultBuilder.java:49)
    at org.openrdf.http.client.HTTPClient.sendTupleQuery(HTTPClient.java:417)
    at org.openrdf.repository.http.HTTPTupleQuery.evaluate(HTTPTupleQuery.java:41)
    at com.ontotext.molto.repositoryHelper.RepositoryUtils.executeQuery(RepositoryUtils.java:71)
    at com.ontotext.molto.repositoryHelper.RepositoryUtils.getAllClassesAndNames(RepositoryUtils.java:133)
    at org.grammaticalframework.eclipse.ontologygrammar.GFOntologyGrammarURLAndTemplatePage.validateURLField(GFOntologyGrammarURLAndTemplatePage.java:224)
    at org.grammaticalframework.eclipse.ontologygrammar.GFOntologyGrammarURLAndTemplatePage.access$0(GFOntologyGrammarURLAndTemplatePage.java:199)
    at org.grammaticalframework.eclipse.ontologygrammar.GFOntologyGrammarURLAndTemplatePage$1.widgetSelected(GFOntologyGrammarURLAndTemplatePage.java:122)
    at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:240)
    at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1258)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:3588)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3209)
    at org.eclipse.jface.window.Window.runEventLoop(Window.java:825)
    at org.eclipse.jface.window.Window.open(Window.java:801)
    at org.eclipse.ui.internal.handlers.WizardHandler$New.executeHandler(WizardHandler.java:257)
    at org.eclipse.ui.internal.handlers.WizardHandler.execute(WizardHandler.java:277)
    at org.eclipse.ui.internal.handlers.HandlerProxy.execute(HandlerProxy.java:293)
    at org.eclipse.core.commands.Command.executeWithChecks(Command.java:476)
    at org.eclipse.core.commands.ParameterizedCommand.executeWithChecks(ParameterizedCommand.java:508)
    at org.eclipse.ui.internal.handlers.HandlerService.executeCommand(HandlerService.java:169)
    at org.eclipse.ui.internal.handlers.SlaveHandlerService.executeCommand(SlaveHandlerService.java:241)
    at org.eclipse.ui.internal.actions.CommandAction.runWithEvent(CommandAction.java:157)
    at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:584)
    at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:501)
    at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:411)
    at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1258)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:3588)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3209)
    at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2696)
    at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2660)
    at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2494)
    at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:674)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
    at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:667)
    at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
    at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:123)
    at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:616)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
    at org.eclipse.equinox.launcher.Main.main(Main.java:1386)

Italian Museums

http://sparql.linkedopendata.it/musei Sucessfully connected.

Linked Life Data

http://linkedlifedata.com/sparql Application hangs.

Open Data Thesaurus

http://vocabulary.semantic-web.at/PoolParty/sparql/OpenData Server responded with an unsupported file format: text/plain

OpenUpLabs Geographic

http://os.services.tso.co.uk/geo/sparql Server returned HTTP response code: 400 for URL: http://rhapp015240:1433/sparql/os-geo

STW Thesaurus for Economics

http://zbw.eu/beta/sparql/stw Successfully connected.

Cancer Genome Atlas

http://hcls.deri.org:8080/openrdf-sesame/repositories/tcga Successfully connected.

WordNet (RKBExplorer)

http://wordnet.rkbexplorer.com/sparql/ Exception while connecting:

!SESSION 2012-08-20 09:33:42.395 -----------------------------------------------
eclipse.buildId=M20110909-1335
java.version=1.6.0_24
java.vendor=Sun Microsystems Inc.
BootLoader constants: OS=linux, ARCH=x86, WS=gtk, NL=en_GB
Framework arguments:  -product org.eclipse.sdk.ide
Command-line arguments:  -product org.eclipse.sdk.ide -data /home/john/repositories/gf-eclipse-plugin/workspace/../workspace-demo -dev file:/home/john/repositories/gf-eclipse-plugin/workspace/.metadata/.plugins/org.eclipse.pde.core/Eclipse Application/dev.properties -os linux -ws gtk -arch x86 -consoleLog

!ENTRY org.eclipse.ui 4 0 2012-08-20 09:58:01.892
!MESSAGE Unhandled event loop exception
!STACK 0
java.lang.NullPointerException
    at org.openrdf.query.impl.TupleQueryResultImpl.<init>(TupleQueryResultImpl.java:48)
    at org.openrdf.query.impl.TupleQueryResultBuilder.getQueryResult(TupleQueryResultBuilder.java:49)
    at org.openrdf.http.client.HTTPClient.sendTupleQuery(HTTPClient.java:417)
    at org.openrdf.repository.http.HTTPTupleQuery.evaluate(HTTPTupleQuery.java:41)
    at com.ontotext.molto.repositoryHelper.RepositoryUtils.executeQuery(RepositoryUtils.java:71)
    at com.ontotext.molto.repositoryHelper.RepositoryUtils.getAllClassesAndNames(RepositoryUtils.java:133)
    at org.grammaticalframework.eclipse.ontologygrammar.GFOntologyGrammarURLAndTemplatePage.validateURLField(GFOntologyGrammarURLAndTemplatePage.java:224)
    at org.grammaticalframework.eclipse.ontologygrammar.GFOntologyGrammarURLAndTemplatePage.access$0(GFOntologyGrammarURLAndTemplatePage.java:199)
    at org.grammaticalframework.eclipse.ontologygrammar.GFOntologyGrammarURLAndTemplatePage$1.widgetSelected(GFOntologyGrammarURLAndTemplatePage.java:122)
    at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:240)
    at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1258)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:3588)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3209)
    at org.eclipse.jface.window.Window.runEventLoop(Window.java:825)
    at org.eclipse.jface.window.Window.open(Window.java:801)
    at org.eclipse.ui.internal.handlers.WizardHandler$New.executeHandler(WizardHandler.java:257)
    at org.eclipse.ui.internal.handlers.WizardHandler.execute(WizardHandler.java:277)
    at org.eclipse.ui.internal.handlers.HandlerProxy.execute(HandlerProxy.java:293)
    at org.eclipse.core.commands.Command.executeWithChecks(Command.java:476)
    at org.eclipse.core.commands.ParameterizedCommand.executeWithChecks(ParameterizedCommand.java:508)
    at org.eclipse.ui.internal.handlers.HandlerService.executeCommand(HandlerService.java:169)
    at org.eclipse.ui.internal.handlers.SlaveHandlerService.executeCommand(SlaveHandlerService.java:241)
    at org.eclipse.ui.internal.actions.CommandAction.runWithEvent(CommandAction.java:157)
    at org.eclipse.ui.internal.actions.CommandAction.run(CommandAction.java:171)
    at org.eclipse.ui.actions.NewWizardDropDownAction.run(NewWizardDropDownAction.java:182)
    at org.eclipse.jface.action.Action.runWithEvent(Action.java:498)
    at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:584)
    at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:501)
    at org.eclipse.jface.action.ActionContributionItem$6.handleEvent(ActionContributionItem.java:452)
    at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1258)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:3588)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3209)
    at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2696)
    at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2660)
    at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2494)
    at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:674)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
    at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:667)
    at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
    at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:123)
    at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:616)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
    at org.eclipse.equinox.launcher.Main.main(Main.java:1386)

WordNet 3.0 (VU Amsterdam)

http://api.talis.com/stores/wordnet/services/sparql

20-Aug-2012 10:00:24 org.apache.commons.httpclient.HttpMethodBase getResponseBody
WARNING: Going to buffer response body of large or unknown size. Using getResponseBodyAsStream instead is recommended.
10116 [main] WARN  org.openrdf.http.client.HTTPClient  - Server reports problem: Remote service returned an error

RxNorm

http://link.informatics.stonybrook.edu/sparql/

112491 [main] WARN  org.openrdf.http.client.HTTPClient  - Server reports problem: Virtuoso 37000 Error SP030: SPARQL compiler, line 1: syntax error at 'group_concat' before '('

SPARQL query:
define sql:big-data-const 0 PREFIX ptop: <http://proton.semanticweb.org/protontop#>PREFIX owl: <http://www.w3.org/2002/07/owl#>PREFIX rdf: <http://www.w3.org/2000/01/rdf-schema#>SELECT ?class (group_concat(?class_label;separator = ' ; ') as ?cnc){ ?class a owl:Class . ?class rdf:label ?class_label . FILTER (!isBlank(?class)) .} group by ?class

...